R Markdown

This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see http://rmarkdown.rstudio.com.

When you click the Knit button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:

Read in data

This now is your clean data with your meta data file only having

## Load packages
library(phyloseq)
library(ape)
library(vegan)
## Loading required package: permute
## Loading required package: lattice
## This is vegan 2.5-6
library(ggplot2)

##Set working directory to bring in files##
setwd("/Users/Carly/Dropbox (Smithsonian)/SI_projects/TX_migBirds/Analyses/")


# this is site by species matrix, need row.names = 1 to have phyloseq read it
# there was an issue with original featureTab. Left over _ in sample names and - between controls instead of _. HAd to manually edit to get file in
featureTab <- read.csv("TxBird_feature_tableCLEAN.csv", header = T, row.names = 1)

# make compatible for phyloseq format
featureTab = otu_table(featureTab, taxa_are_rows = TRUE)
## 529 taxa by 18 samples
dim(featureTab)
## [1] 522  18
# Read taxonomy info in, make matrix and compatible for phyloseq
## This file will be subset to only include the taxonomy that makes to the features (OTUs, ASVs)
taxonomy <- tax_table(as.matrix(read.csv("TxBird_taxonomy.csv", row.names = 1)))


# Read metadata info in, make compatible for phyloseq
## NOTE: we calculated alpha diversity estimates and added to _meta file and called it now _alpha. 
## You may need to change row.names = if your sampleID is in a different column. Ours is in column 2

meta_data <- sample_data(read.csv("TxBird_meta_alpha.csv", header = T, row.names = 2))


# Read in sequence data, may need if you want to look at or subset the DNA sequences at some point
library(Biostrings)
## Loading required package: BiocGenerics
## Loading required package: parallel
## 
## Attaching package: 'BiocGenerics'
## The following objects are masked from 'package:parallel':
## 
##     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
##     clusterExport, clusterMap, parApply, parCapply, parLapply,
##     parLapplyLB, parRapply, parSapply, parSapplyLB
## The following objects are masked from 'package:stats':
## 
##     IQR, mad, sd, var, xtabs
## The following objects are masked from 'package:base':
## 
##     anyDuplicated, append, as.data.frame, basename, cbind,
##     colMeans, colnames, colSums, dirname, do.call, duplicated,
##     eval, evalq, Filter, Find, get, grep, grepl, intersect,
##     is.unsorted, lapply, lengths, Map, mapply, match, mget, order,
##     paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,
##     Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort,
##     table, tapply, union, unique, unsplit, which, which.max,
##     which.min
## Loading required package: S4Vectors
## Loading required package: stats4
## 
## Attaching package: 'S4Vectors'
## The following object is masked from 'package:base':
## 
##     expand.grid
## Loading required package: IRanges
## 
## Attaching package: 'IRanges'
## The following object is masked from 'package:phyloseq':
## 
##     distance
## Loading required package: XVector
## 
## Attaching package: 'Biostrings'
## The following object is masked from 'package:ape':
## 
##     complement
## The following object is masked from 'package:base':
## 
##     strsplit
seqs <- readDNAStringSet("TxBird_feature_DNAsequence.fasta")


# You can also add a phylogenetic tree here, if you have one
# library(ape)
# tree = read.tree("FinalRFiles/exported-tree/SalAMPtree.nwk")

# Merge it all together

sample_names(meta_data)
##  [1] "TX202145335" "TX240130218" "TX240130255" "TX252145317" "TX263105336"
##  [6] "TX263105978" "TX272136690" "TX272136698" "TX272136699" "TX279103530"
## [11] "TX279103554" "TX279103561" "TX279103567" "TX279103583" "TX279103586"
## [16] "TX281118809" "TX281118812" "TX281118835"
Tx <- merge_phyloseq(featureTab, taxonomy, meta_data, seqs) #tree)

Tx
## phyloseq-class experiment-level object
## otu_table()   OTU Table:         [ 522 taxa and 18 samples ]
## sample_data() Sample Data:       [ 18 samples by 21 sample variables ]
## tax_table()   Taxonomy Table:    [ 522 taxa by 7 taxonomic ranks ]
## refseq()      DNAStringSet:      [ 522 reference sequences ]
sample_names(Tx)
##  [1] "TX202145335" "TX240130218" "TX240130255" "TX252145317" "TX263105336"
##  [6] "TX263105978" "TX272136690" "TX272136698" "TX272136699" "TX279103530"
## [11] "TX279103554" "TX279103561" "TX279103567" "TX279103583" "TX279103586"
## [16] "TX281118809" "TX281118812" "TX281118835"
## Total of 175,377 sequences across 18 samples
sum(sample_sums(Tx))
## [1] 175377
sort(sample_sums(Tx))
## TX279103567 TX279103530 TX279103561 TX240130218 TX281118812 TX202145335 
##         984        1068        1453        2260        3643        4471 
## TX252145317 TX263105978 TX263105336 TX279103586 TX240130255 TX281118809 
##        4636        5037        5342        6698        7820        9721 
## TX279103583 TX279103554 TX272136699 TX272136690 TX281118835 TX272136698 
##       11365       13214       13952       16125       23946       43642
## BUT, remember we have to analyze the rarefied dataset because of sequencing coverage issues

Tx = rarefy_even_depth(Tx, replace=FALSE, rngseed = 711)
## `set.seed(711)` was used to initialize repeatable random subsampling.
## Please record this for your records so others can reproduce.
## Try `set.seed(711); .Random.seed` for the full vector
## ...
## 22OTUs were removed because they are no longer 
## present in any sample after random subsampling
## ...
## In the end, in the results section I would report we had 17,712 high quality sequences we analyzed after normalization to even sequencing depth. 
sum(sample_sums(Tx))
## [1] 17712
### MAKE dataframe of metadata for alpha and beta analyses. This makes sure your metadata are in same order as your feature table

dfTx <- as(sample_data(Tx), "data.frame")

## We also will be interested in just the cloacal swab data for some comparisons and also just the Oven bird (also samples swaisons)
## Let's make these files now for later

TxC <- subset_samples(Tx, Type == "CloacalSwab")
dfTxC <- as(sample_data(TxC), "data.frame")

TxO <- subset_samples(Tx, Species == "OVEN")
dfTxO <- as(sample_data(TxO), "data.frame")

Alpha diversity

## Alpha

str(dfTx)
## 'data.frame':    18 obs. of  21 variables:
##  $ SampleID         : Factor w/ 18 levels "TX202145335",..: 1 2 3 4 5 6 7 8 9 10 ...
##  $ BandNumber       : int  202145335 240130218 240130255 252145317 263105336 263105978 272136690 272136698 272136699 279103530 ...
##  $ CollectionDate   : Factor w/ 14 levels "4/19/16","4/19/19",..: 14 1 3 10 7 5 8 9 9 2 ...
##  $ Species          : Factor w/ 2 levels "OVEN","SWTH": 1 1 1 1 1 1 1 1 1 2 ...
##  $ Type             : Factor w/ 2 levels "CloacalSwab",..: 2 2 2 2 2 2 1 1 1 1 ...
##  $ Duplicate        : Factor w/ 2 levels "No","Yes": 1 1 1 1 1 1 2 2 2 1 ...
##  $ Prep             : Factor w/ 1 level "Same": 1 1 1 1 1 1 1 1 1 1 ...
##  $ Sample_or_Control: Factor w/ 1 level "True Sample": 1 1 1 1 1 1 1 1 1 1 ...
##  $ quant_reading    : num  10 9 9.3 10 9 10 0.297 21.5 0.577 0.058 ...
##  $ is.neg           : logi  FALSE FALSE FALSE FALSE FALSE FALSE ...
##  $ S.obs            : int  127 98 69 83 100 162 69 108 117 36 ...
##  $ S.chao1          : int  127 98 69 83 100 162 69 108 117 36 ...
##  $ se.chao1.x       : num  0 0 0 0 0 ...
##  $ S.ACE            : num  127 98 69 83 100 ...
##  $ se.ACE.x         : num  5.2 4.64 3.96 4.31 4.54 ...
##  $ sample_sums.Tx5. : int  4471 2260 7820 4636 5342 5037 16125 43642 13952 1068 ...
##  $ S.obs_rare       : int  115 96 57 75 89 147 63 45 112 36 ...
##  $ S.chao1_rare     : num  129.9 97.4 59.9 79.6 96.6 ...
##  $ se.chao1.y       : num  8.21 1.74 2.58 3.82 4.98 ...
##  $ S.ACE_rare       : num  125.7 97.6 62.5 80.5 98.8 ...
##  $ se.ACE.y         : num  4.25 4.45 3.23 3.74 4.03 ...
## let's look at alpha estimates between cloacal swabs and fecal samples
## Remember we are using the rarefied estimates since we had so much variation in sequencing coverage
ggplot(data = dfTx, aes(x=Type, y=S.obs_rare))+geom_boxplot()+theme_bw()+theme_classic()+
  theme(text = element_text(size = 20)) + ylab("Bacterial ASV richness") + xlab("")

## plot made with base R, quicker to write, but not as great at modifying for pub as ggplot figures
plot(dfTx$S.obs_rare ~ dfTx$Type)

## how about alpha across samples
plot(dfTx$S.obs_rare ~ dfTx$SampleID)

## make with ggplot instead
ggplot(data = dfTx, aes(x=as.factor(SampleID), y=S.obs_rare))+geom_bar(stat = "identity")+theme_bw()+theme_classic()+
  theme(text = element_text(size = 20)) + ylab("Bacterial ASV richness") + xlab("") + theme(axis.text.x = element_text(angle = 90, hjust = 1))

## How about between bird species, but we need to subset to only cloacal swabs for this comparison. So we use the cloacal swab data we subsetted above
## Fecals were only taken for Oven birds

ggplot(data = dfTxC, aes(x=Species, y=S.obs_rare))+geom_boxplot()+theme_bw()+theme_classic()+
  theme(text = element_text(size = 20)) + ylab("Bacterial ASV richness") + xlab("")

## Oh, so if oven birds were the only bird with both fecals and clocal swabs then we should subset to them when look at differencees between fecals and cloacals. 

ggplot(data = dfTxO, aes(x=Type, y=S.obs_rare))+geom_boxplot()+theme_bw()+theme_classic()+
  theme(text = element_text(size = 20)) + ylab("Bacterial ASV richness") + xlab("")

### STATS for between cloacal and fecals and STATs for between bird species 


#### CLOACAL vs FECES in Oven birds
## look at distribution of species richness values
## looks normal
hist(dfTxO$S.obs_rare)

## p value is above 0.05, so data is normally distributed
shapiro.test(dfTxO$S.obs_rare)
## 
##  Shapiro-Wilk normality test
## 
## data:  dfTxO$S.obs_rare
## W = 0.9507, p-value = 0.6472
## You can try log10(dfTx$S.obs_rare)
## You can try srqt like this to make data normal, either of those usually work for me


library(car)
## Loading required package: carData
## testing for homogeneity of variance
## p value is above 0.05, so data similar variances
leveneTest(S.obs_rare~Type, data=dfTxO)
## Levene's Test for Homogeneity of Variance (center = median)
##       Df F value Pr(>F)
## group  1   0.398 0.5423
##       10
## Good to go for t-test and met assumptions
modeAlphaO <- t.test(S.obs_rare~Type, data=dfTxO)
modeAlphaO
## 
##  Welch Two Sample t-test
## 
## data:  S.obs_rare by Type
## t = -0.77174, df = 8.5446, p-value = 0.4611
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
##  -72.51278  35.84611
## sample estimates:
## mean in group CloacalSwab       mean in group Fecal 
##                  78.16667                  96.50000
## So, says this is not different in alpha between cloacal and fecals
ggplot(data = dfTxO, aes(x=Type, y=S.obs_rare))+geom_boxplot()+theme_bw()+theme_classic()+
  theme(text = element_text(size = 20)) + ylab("Bacterial ASV richness") + xlab("")

## Now for reasons of showing how to do stats with 2+ levels (ANOVA), let's make a third level to compare 

str(dfTx)
## 'data.frame':    18 obs. of  21 variables:
##  $ SampleID         : Factor w/ 18 levels "TX202145335",..: 1 2 3 4 5 6 7 8 9 10 ...
##  $ BandNumber       : int  202145335 240130218 240130255 252145317 263105336 263105978 272136690 272136698 272136699 279103530 ...
##  $ CollectionDate   : Factor w/ 14 levels "4/19/16","4/19/19",..: 14 1 3 10 7 5 8 9 9 2 ...
##  $ Species          : Factor w/ 2 levels "OVEN","SWTH": 1 1 1 1 1 1 1 1 1 2 ...
##  $ Type             : Factor w/ 2 levels "CloacalSwab",..: 2 2 2 2 2 2 1 1 1 1 ...
##  $ Duplicate        : Factor w/ 2 levels "No","Yes": 1 1 1 1 1 1 2 2 2 1 ...
##  $ Prep             : Factor w/ 1 level "Same": 1 1 1 1 1 1 1 1 1 1 ...
##  $ Sample_or_Control: Factor w/ 1 level "True Sample": 1 1 1 1 1 1 1 1 1 1 ...
##  $ quant_reading    : num  10 9 9.3 10 9 10 0.297 21.5 0.577 0.058 ...
##  $ is.neg           : logi  FALSE FALSE FALSE FALSE FALSE FALSE ...
##  $ S.obs            : int  127 98 69 83 100 162 69 108 117 36 ...
##  $ S.chao1          : int  127 98 69 83 100 162 69 108 117 36 ...
##  $ se.chao1.x       : num  0 0 0 0 0 ...
##  $ S.ACE            : num  127 98 69 83 100 ...
##  $ se.ACE.x         : num  5.2 4.64 3.96 4.31 4.54 ...
##  $ sample_sums.Tx5. : int  4471 2260 7820 4636 5342 5037 16125 43642 13952 1068 ...
##  $ S.obs_rare       : int  115 96 57 75 89 147 63 45 112 36 ...
##  $ S.chao1_rare     : num  129.9 97.4 59.9 79.6 96.6 ...
##  $ se.chao1.y       : num  8.21 1.74 2.58 3.82 4.98 ...
##  $ S.ACE_rare       : num  125.7 97.6 62.5 80.5 98.8 ...
##  $ se.ACE.y         : num  4.25 4.45 3.23 3.74 4.03 ...
## We have species and type factors we can combine to make another set of levels

dfTx$SpeciesType <- as.factor(paste(dfTx$Species, dfTx$Type))
levels(dfTx$SpeciesType)
## [1] "OVEN CloacalSwab" "OVEN Fecal"       "SWTH CloacalSwab"
## Can add this to phyloseq object also
sample_data(Tx)$SpeciesType <- as.factor(paste(sample_data(Tx)$Species, sample_data(Tx)$Type))


shapiro.test(dfTx$S.obs_rare)
## 
##  Shapiro-Wilk normality test
## 
## data:  dfTx$S.obs_rare
## W = 0.91158, p-value = 0.09175
leveneTest(S.obs_rare~SpeciesType, data=dfTx)
## Levene's Test for Homogeneity of Variance (center = median)
##       Df F value Pr(>F)
## group  2  0.7209 0.5024
##       15
## good for ANOVA
modeAlpha2 <- aov(S.obs_rare~SpeciesType, data=dfTx)
summary(modeAlpha2)
##             Df Sum Sq Mean Sq F value Pr(>F)
## SpeciesType  2   5862    2931   2.341   0.13
## Residuals   15  18776    1252
## So, says this is not different in alpha between cloacal and fecals
ggplot(data = dfTx, aes(x=SpeciesType, y=S.obs_rare))+geom_boxplot()+theme_bw()+theme_classic()+
  theme(text = element_text(size = 20)) + ylab("Bacterial ASV richness") + xlab("")

## But, if sig then run Tukey's, can see swth cloacal almost differnt to oven fecal, which we can see in the plot
TukeyHSD(modeAlpha2)
##   Tukey multiple comparisons of means
##     95% family-wise confidence level
## 
## Fit: aov(formula = S.obs_rare ~ SpeciesType, data = dfTx)
## 
## $SpeciesType
##                                        diff       lwr       upr     p adj
## OVEN Fecal-OVEN CloacalSwab        18.33333 -34.72382 71.390485 0.6500414
## SWTH CloacalSwab-OVEN CloacalSwab -25.66667 -78.72382 27.390485 0.4399985
## SWTH CloacalSwab-OVEN Fecal       -44.00000 -97.05715  9.057152 0.1123501
#### BETWEEN SPECIES STATS for alpha, remember need just the cloacal data for this

## not normal, so transform, normal with log10 transformation, use this in stats then
shapiro.test(dfTxC$S.obs_rare)
## 
##  Shapiro-Wilk normality test
## 
## data:  dfTxC$S.obs_rare
## W = 0.81489, p-value = 0.01391
shapiro.test(log10(dfTxC$S.obs_rare))
## 
##  Shapiro-Wilk normality test
## 
## data:  log10(dfTxC$S.obs_rare)
## W = 0.93273, p-value = 0.41
leveneTest(log10(S.obs_rare)~Species, data=dfTxC)
## Levene's Test for Homogeneity of Variance (center = median)
##       Df F value Pr(>F)
## group  1  0.4805  0.504
##       10
## Good to go for t-test and met assumptions with log10
modeAlphaC <- t.test(log10(S.obs_rare)~Species, data=dfTxC)
modeAlphaC
## 
##  Welch Two Sample t-test
## 
## data:  log10(S.obs_rare) by Species
## t = 1.0574, df = 8.4339, p-value = 0.3197
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
##  -0.1532966  0.4172659
## sample estimates:
## mean in group OVEN mean in group SWTH 
##           1.826989           1.695005
## So not different, can visualize again
ggplot(data = dfTxC, aes(x=Species, y=S.obs_rare))+geom_boxplot()+theme_bw()+theme_classic()+
  theme(text = element_text(size = 20)) + ylab("Bacterial ASV richness") + xlab("")

##Can visualize also on log10 to see what stats see
ggplot(data = dfTxC, aes(x=Species, y=log10(S.obs_rare)))+geom_boxplot()+theme_bw()+theme_classic()+
  theme(text = element_text(size = 20)) + ylab("Bacterial ASV richness") + xlab("")

## You can then go through with other alpha diversity estimates as desired
## I do not suggest analyzing Shannon as it voliates test assumptions since it is generally on scale to 1-7 and not truly numeric, need to analyze with special statistics
## I prefer species richness and faith's phylogenetic diversity. Evenness may also be of interest too. But, don't throw the kitchen sink at it. Think about why you are analyzing an alpha metric and what it would mean biologically before you start analyzing

Beta diversity

### NOTE: When you do jaccard, it is critical that you put binary = T, so that it is looking at presence absence data. 

jacc_tx <- phyloseq::distance(Tx, "jaccard", binary = T)
jacc.ord <- ordinate(Tx, method = "PCoA", jacc_tx)

## Look at our three levels we made earlier, species type
p_jacc <- plot_ordination(Tx, jacc.ord, color = "Type", shape = "Species")
p_jacc + geom_point(size = 4)  +theme_bw() +theme_classic()+ 
  theme(text = element_text(size = 20))+ stat_ellipse(aes(group = SpeciesType))

## Probably better to plot like this
p_jacc2 <- plot_ordination(Tx, jacc.ord, color = "SpeciesType")
p_jacc2 + geom_point(size = 4)  +theme_bw() +theme_classic()+ 
  theme(text = element_text(size = 20))+ stat_ellipse(aes(group = SpeciesType))

### STATS
jacc_adonisST <- adonis(jacc_tx ~ SpeciesType, data = dfTx)
jacc_adonisST
## 
## Call:
## adonis(formula = jacc_tx ~ SpeciesType, data = dfTx) 
## 
## Permutation: free
## Number of permutations: 999
## 
## Terms added sequentially (first to last)
## 
##             Df SumsOfSqs MeanSqs F.Model     R2 Pr(>F)    
## SpeciesType  2    1.5520 0.77599  2.1837 0.2255  0.001 ***
## Residuals   15    5.3303 0.35535         0.7745           
## Total       17    6.8823                 1.0000           
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
library(pairwiseAdonis)
## Loading required package: cluster
## So, looks like a type effect we are picking up here, fecals are different
pairwise.adonis(jacc_tx, dfTx$SpeciesType)
##                                  pairs Df SumsOfSqs  F.Model        R2
## 1       OVEN Fecal vs OVEN CloacalSwab  1 0.8575601 2.421652 0.1949541
## 2       OVEN Fecal vs SWTH CloacalSwab  1 1.0255301 2.994420 0.2304389
## 3 OVEN CloacalSwab vs SWTH CloacalSwab  1 0.4448820 1.204153 0.1074738
##   p.value p.adjusted sig
## 1   0.002      0.006   *
## 2   0.004      0.012   .
## 3   0.200      0.600
### Let's see if there is a species effect we are missing because of the huge effect of fecal vs cloaca

jacc_sp <- phyloseq::distance(TxC, "jaccard", binary = T)
jacc.ordS <- ordinate(TxC, method = "PCoA", jacc_sp)

p_jaccS <- plot_ordination(TxC, jacc.ordS, color = "Species", shape = "Species")
p_jaccS + geom_point(size = 4)  +theme_bw() +theme_classic()+ 
  theme(text = element_text(size = 20))+ stat_ellipse(aes(group = Species))

### STATS, no species effect, low sample size though
jacc_adonisSp <- adonis(jacc_sp ~ Species, data = dfTxC)
jacc_adonisSp
## 
## Call:
## adonis(formula = jacc_sp ~ Species, data = dfTxC) 
## 
## Permutation: free
## Number of permutations: 999
## 
## Terms added sequentially (first to last)
## 
##           Df SumsOfSqs MeanSqs F.Model      R2 Pr(>F)
## Species    1    0.4449 0.44488  1.2042 0.10747  0.239
## Residuals 10    3.6946 0.36946         0.89253       
## Total     11    4.1394                 1.00000
## Ok, last bit, how about between oven cloacal and oven fecal

jacc_t <- phyloseq::distance(TxO, "jaccard", binary = T)
jacc.ordO <- ordinate(TxO, method = "PCoA", jacc_t)

p_jaccT <- plot_ordination(TxO, jacc.ordO, color = "Type", shape = "Type")
p_jaccT + geom_point(size = 4)  +theme_bw() +theme_classic()+ 
  theme(text = element_text(size = 20))+ stat_ellipse(aes(group = Type))

### STATS, no species effect, low sample size though
jacc_adonisT <- adonis(jacc_t ~ Type, data = dfTxO)
jacc_adonisT
## 
## Call:
## adonis(formula = jacc_t ~ Type, data = dfTxO) 
## 
## Permutation: free
## Number of permutations: 999
## 
## Terms added sequentially (first to last)
## 
##           Df SumsOfSqs MeanSqs F.Model      R2 Pr(>F)   
## Type       1    0.8576 0.85756  2.4217 0.19495  0.004 **
## Residuals 10    3.5412 0.35412         0.80505          
## Total     11    4.3988                 1.00000          
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## But, I feel like this would be the plot I would show, and I would do the stats separately. Species effect with just cloacal samples, and type effect of just oven birds

## Dress the figure up a bit
p_jacc2 <- plot_ordination(Tx, jacc.ord, color = "SpeciesType", shape = "SpeciesType")
p_jacc2 + geom_point(size = 4)  +theme_bw() +theme_classic()+ 
  theme(text = element_text(size = 20))+ stat_ellipse(aes(group = SpeciesType)) +
  labs("Sample type") + scale_color_manual(values = c("blue", "chocolate4", "green"), name = "Sample type") +
  scale_shape_manual(values = c(17, 19, 15), name = "Sample type")

## Can repeat these analyses with Bray-Curtis, etc. I prefer Jaccard and Bray-Curtis as defaults. One looking at presence-absence differces (Jaccard) and one considered relative abundances and differences (Bray-Curtis). Unifrac and weigthed unifrac as useful too i fyou have a phylogenetic tree.

Relative abundance and taxonomy distribution

## taxonomy table of just cloacal swabs, was interested in this for some reason
## leaving code in case of interest
tax <- as(tax_table(TxC), "matrix")
#write.csv(tax, "TxBird_taxonomyCloacaAfterFiltering.csv")

rank_names(Tx)
## [1] "Kingdom" "Phylum"  "Class"   "Order"   "Family"  "Genus"   "Species"
## Distribution across samples of some genus of bacterial pathogens of concerns.
## Each bar means it is a different ASV
Tx_diplor = subset_taxa(Tx, Genus == "Diplorickettsia")

plot_bar(Tx_diplor)
## Warning in psmelt(physeq): The sample variables: 
## Species
##  have been renamed to: 
## sample_Species
## to avoid conflicts with taxonomic rank names.

Tx_myco = subset_taxa(Tx, Genus == "Mycobacterium")

plot_bar(Tx_myco)
## Warning in psmelt(physeq): The sample variables: 
## Species
##  have been renamed to: 
## sample_Species
## to avoid conflicts with taxonomic rank names.

## Using pipes for this code
## Much better than creating lots of objects like old code I had

library(magrittr)
library(dplyr)
## 
## Attaching package: 'dplyr'
## The following object is masked from 'package:car':
## 
##     recode
## The following objects are masked from 'package:Biostrings':
## 
##     collapse, intersect, setdiff, setequal, union
## The following object is masked from 'package:XVector':
## 
##     slice
## The following objects are masked from 'package:IRanges':
## 
##     collapse, desc, intersect, setdiff, slice, union
## The following objects are masked from 'package:S4Vectors':
## 
##     first, intersect, rename, setdiff, setequal, union
## The following objects are masked from 'package:BiocGenerics':
## 
##     combine, intersect, setdiff, union
## The following objects are masked from 'package:stats':
## 
##     filter, lag
## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union
Tx_phylum <- Tx %>%
  tax_glom(taxrank = "Phylum") %>%                     # agglomerate at phylum level
  transform_sample_counts(function(x) {x/sum(x)} ) %>% # Transform to rel. abundance
  psmelt() %>%                                         # Melt to long format
  arrange(Phylum)                                      # Sort data frame alphabetically 
## Warning in psmelt(.): The sample variables: 
## Species
##  have been renamed to: 
## sample_Species
## to avoid conflicts with taxonomic rank names.
## get warning message, no worries

p_RA <- ggplot(data=Tx_phylum, aes(x=Sample, y=Abundance, fill=Phylum))

p_RA + geom_bar(aes(), stat="identity", position="stack")  + 
  ylab("Relative abundance (% of sequences)") +theme_classic()  + theme_bw()  +
  theme_classic()+ labs(x = "")+ theme(text = element_text(size = 18))

## better to make your own colors
cbPalette <- c("black", "mediumpurple", "#999999", "#CC79A7", "#56B4E9", "#009E73", "aquamarine2", "#F0E442","#0072B2","#E69F00","#D55E00" , "gray44", "darkolivegreen1")

p_RA + geom_bar(aes(), stat="identity", position="stack")  + 
  ylab("Relative abundance (% of sequences)") +theme_classic()  + theme_bw()  +
  theme_classic()+ labs(x = "")+ theme(text = element_text(size = 18)) + scale_fill_manual(values=cbPalette,name="Phylum")

## Let's merge by SpeciesType

Tx_phylum <- Tx %>%
  tax_glom(taxrank = "Phylum") %>%  # agglomerate at phylum level
  merge_samples("SpeciesType") %>%  # merge samples on variable of interest
  transform_sample_counts(function(x) {x/sum(x)} ) %>% # Transform to rel. abundance
  psmelt() %>%                                         # Melt to long format
  arrange(Phylum)  
## Warning in psmelt(.): The sample variables: 
## Species
##  have been renamed to: 
## sample_Species
## to avoid conflicts with taxonomic rank names.
ggplot(data=Tx_phylum, aes(x=Sample, y=Abundance, fill=Phylum)) +geom_bar(aes(), stat="identity", position="stack")  + 
  ylab("Relative abundance (% of sequences)") +theme_classic() + theme_bw()  +
  theme_classic()+ labs(x = "")+ theme(text = element_text(size = 18)) + scale_fill_manual(values=cbPalette,name="Phylum") + theme(axis.text.x = element_text(angle = 50, vjust = 0.5))

## How about at genus level?
## NOTE: we need to filter low abundance ASVs
## This will take a little time to run depending on dataset
## NOTE: when you get to these lower tax levels you need to think about tax_glom and the NArm = T or F option. See the help file of tax_glom. I feel like you shouldn't remove taxa that don't have a genus assignment, so I prefer NArm = F when doing analyses, but for making the plots NArm = T (default) is preferred or otherwise challenging to plot. Still thinking through this, but a note that taxa are removed that don't have genus level assignments when you do tax_glom at genus level

Tx_genus05 <- Tx %>%
  tax_glom(taxrank = "Genus", NArm = T) %>%  # agglomerate at phylum level
  merge_samples("SpeciesType") %>%  # merge samples on variable of interest
  transform_sample_counts(function(x) {x/sum(x)} ) %>% # Transform to rel. abundance
  psmelt() %>%                                         # Melt to long format
  filter(Abundance > 0.05) %>% 
  arrange(Genus)  
## Warning in psmelt(.): The sample variables: 
## Species
##  have been renamed to: 
## sample_Species
## to avoid conflicts with taxonomic rank names.
## Can play around with the filter number. Could try 1% or 5%, etc


ggplot(data=Tx_genus05, aes(x=Sample, y=Abundance, fill=Genus)) +geom_bar(aes(), stat="identity", position="stack")  + 
  ylab("Relative abundance (% of sequences)") +theme_classic() + theme_bw()  +
  theme_classic()+ labs(x = "")+ theme(text = element_text(size = 18)) + scale_fill_manual(values=cbPalette,name="Genus") + theme(axis.text.x = element_text(angle = 50, vjust = 0.5))

Tx_genus01 <- Tx %>%
  tax_glom(taxrank = "Genus") %>%  # agglomerate at phylum level
  merge_samples("SpeciesType") %>%  # merge samples on variable of interest
  transform_sample_counts(function(x) {x/sum(x)} ) %>% # Transform to rel. abundance
  psmelt() %>%                                         # Melt to long format
  filter(Abundance > 0.01) %>% 
  arrange(Genus)  
## Warning in psmelt(.): The sample variables: 
## Species
##  have been renamed to: 
## sample_Species
## to avoid conflicts with taxonomic rank names.
## Will let use default colors for now, would need to provide many more colors to get cbPalette to fill in.

ggplot(data=Tx_genus01, aes(x=Sample, y=Abundance, fill=Genus)) +geom_bar(aes(), stat="identity", position="stack")  + 
  ylab("Relative abundance (% of sequences)") +theme_classic() + theme_bw()  +
  theme_classic()+ labs(x = "")+ theme(text = element_text(size = 18)) + theme(axis.text.x = element_text(angle = 50, vjust = 0.5))

## Remove legend so can see plot
ggplot(data=Tx_genus01, aes(x=Sample, y=Abundance, fill=Genus)) +geom_bar(aes(), stat="identity", position="stack")  + 
  ylab("Relative abundance (% of sequences)") +theme_classic() + theme_bw()  +
  theme_classic()+ labs(x = "")+ theme(text = element_text(size = 18)) + theme(axis.text.x = element_text(angle = 50, vjust = 0.5)) + theme(legend.position = "none")

## Ok, not totally in love with this figure. Would need some tweaks or annotation in legend 

## or this addition might help

Tx_genus2 <- Tx %>%
  tax_glom(taxrank = "Genus") %>%  # agglomerate at phylum level
  merge_samples("SpeciesType") %>%  # merge samples on variable of interest
  transform_sample_counts(function(x) {x/sum(x)} ) %>% # Transform to rel. abundance
  psmelt() %>%                                         # Melt to long format
  arrange(Genus)  
## Warning in psmelt(.): The sample variables: 
## Species
##  have been renamed to: 
## sample_Species
## to avoid conflicts with taxonomic rank names.
Tx_genus2$Genus <- as.character(Tx_genus2$Genus) #convert to character

Tx_genus2$Genus[Tx_genus2$Abundance < 0.05] <- "Genera < 5% abund."

ggplot(data=Tx_genus2, aes(x=Sample, y=Abundance, fill=Genus)) +geom_bar(aes(), stat="identity", position="stack")  + 
  ylab("Relative abundance (% of sequences)") +theme_classic() + theme_bw()  +
  theme_classic()+ labs(x = "")+ theme(text = element_text(size = 18))  + theme(axis.text.x = element_text(angle = 50, vjust = 0.5)) + scale_fill_manual(values=cbPalette,name="Genus")

Differential abundances

####    DIFFERNTIAL ABUNDANCE TESTING   ##########


library(DAtest)
## DAtest version 2.7.15
## More here: https://github.com/Russel88/DAtest/wiki

## DAtest does not perform well with ASV level. 
## Posted on github https://github.com/Russel88/DAtest/issues/9
## Basically can only look at FPR and use that to rank. 

## For this example let's look at differences in abundances of ASVs and of phylum between fecal and swabs as we know there are differences there. 

## Change min number of samples based on your data. Not a lot of samples here so doing low for 3
TxODA <- preDA(TxO, min.samples = 3, min.reads = 1, min.abundance = 0) 
## 368 features grouped as 'Others' in the output
## Testing DA for 133 ASVs
TxODA 
## phyloseq-class experiment-level object
## otu_table()   OTU Table:         [ 133 taxa and 12 samples ]
## sample_data() Sample Data:       [ 12 samples by 21 sample variables ]
## tax_table()   Taxonomy Table:    [ 133 taxa by 7 taxonomic ranks ]
## Will take some time to run depending on data size
mytest <- testDA(TxODA, predictor = "Type")
## Running on 3 cores
## predictor is assumed to be a categorical variable with 2 levels: CloacalSwab, Fecal
## Spikeing...
## Testing 28 methods 20 times each...
## 
  |                                                                       
  |                                                                 |   0%
  |                                                                       
  |                                                                 |   1%
  |                                                                       
  |=                                                                |   1%
  |                                                                       
  |=                                                                |   2%
  |                                                                       
  |==                                                               |   2%
  |                                                                       
  |==                                                               |   3%
  |                                                                       
  |==                                                               |   4%
  |                                                                       
  |===                                                              |   4%
  |                                                                       
  |===                                                              |   5%
  |                                                                       
  |====                                                             |   6%
  |                                                                       
  |====                                                             |   7%
  |                                                                       
  |=====                                                            |   7%
  |                                                                       
  |=====                                                            |   8%
  |                                                                       
  |======                                                           |   9%
  |                                                                       
  |======                                                           |  10%
  |                                                                       
  |=======                                                          |  10%
  |                                                                       
  |=======                                                          |  11%
  |                                                                       
  |========                                                         |  12%
  |                                                                       
  |========                                                         |  13%
  |                                                                       
  |=========                                                        |  13%
  |                                                                       
  |=========                                                        |  14%
  |                                                                       
  |==========                                                       |  15%
  |                                                                       
  |==========                                                       |  16%
  |                                                                       
  |===========                                                      |  16%
  |                                                                       
  |===========                                                      |  17%
  |                                                                       
  |===========                                                      |  18%
  |                                                                       
  |============                                                     |  18%
  |                                                                       
  |============                                                     |  19%
  |                                                                       
  |=============                                                    |  19%
  |                                                                       
  |=============                                                    |  20%
  |                                                                       
  |=============                                                    |  21%
  |                                                                       
  |==============                                                   |  21%
  |                                                                       
  |==============                                                   |  22%
  |                                                                       
  |===============                                                  |  22%
  |                                                                       
  |===============                                                  |  23%
  |                                                                       
  |===============                                                  |  24%
  |                                                                       
  |================                                                 |  24%
  |                                                                       
  |================                                                 |  25%
  |                                                                       
  |=================                                                |  26%
  |                                                                       
  |=================                                                |  27%
  |                                                                       
  |==================                                               |  27%
  |                                                                       
  |==================                                               |  28%
  |                                                                       
  |===================                                              |  29%
  |                                                                       
  |===================                                              |  30%
  |                                                                       
  |====================                                             |  30%
  |                                                                       
  |====================                                             |  31%
  |                                                                       
  |=====================                                            |  32%
  |                                                                       
  |=====================                                            |  33%
  |                                                                       
  |======================                                           |  33%
  |                                                                       
  |======================                                           |  34%
  |                                                                       
  |=======================                                          |  35%
  |                                                                       
  |=======================                                          |  36%
  |                                                                       
  |========================                                         |  36%
  |                                                                       
  |========================                                         |  37%
  |                                                                       
  |========================                                         |  38%
  |                                                                       
  |=========================                                        |  38%
  |                                                                       
  |=========================                                        |  39%
  |                                                                       
  |==========================                                       |  39%
  |                                                                       
  |==========================                                       |  40%
  |                                                                       
  |==========================                                       |  41%
  |                                                                       
  |===========================                                      |  41%
  |                                                                       
  |===========================                                      |  42%
  |                                                                       
  |============================                                     |  42%
  |                                                                       
  |============================                                     |  43%
  |                                                                       
  |============================                                     |  44%
  |                                                                       
  |=============================                                    |  44%
  |                                                                       
  |=============================                                    |  45%
  |                                                                       
  |==============================                                   |  46%
  |                                                                       
  |==============================                                   |  47%
  |                                                                       
  |===============================                                  |  47%
  |                                                                       
  |===============================                                  |  48%
  |                                                                       
  |================================                                 |  49%
  |                                                                       
  |================================                                 |  50%
  |                                                                       
  |=================================                                |  50%
  |                                                                       
  |=================================                                |  51%
  |                                                                       
  |==================================                               |  52%
  |                                                                       
  |==================================                               |  53%
  |                                                                       
  |===================================                              |  53%
  |                                                                       
  |===================================                              |  54%
  |                                                                       
  |====================================                             |  55%
  |                                                                       
  |====================================                             |  56%
  |                                                                       
  |=====================================                            |  56%
  |                                                                       
  |=====================================                            |  57%
  |                                                                       
  |=====================================                            |  58%
  |                                                                       
  |======================================                           |  58%
  |                                                                       
  |======================================                           |  59%
  |                                                                       
  |=======================================                          |  59%
  |                                                                       
  |=======================================                          |  60%
  |                                                                       
  |=======================================                          |  61%
  |                                                                       
  |========================================                         |  61%
  |                                                                       
  |========================================                         |  62%
  |                                                                       
  |=========================================                        |  62%
  |                                                                       
  |=========================================                        |  63%
  |                                                                       
  |=========================================                        |  64%
  |                                                                       
  |==========================================                       |  64%
  |                                                                       
  |==========================================                       |  65%
  |                                                                       
  |===========================================                      |  66%
  |                                                                       
  |===========================================                      |  67%
  |                                                                       
  |============================================                     |  67%
  |                                                                       
  |============================================                     |  68%
  |                                                                       
  |=============================================                    |  69%
  |                                                                       
  |=============================================                    |  70%
  |                                                                       
  |==============================================                   |  70%
  |                                                                       
  |==============================================                   |  71%
  |                                                                       
  |===============================================                  |  72%
  |                                                                       
  |===============================================                  |  73%
  |                                                                       
  |================================================                 |  73%
  |                                                                       
  |================================================                 |  74%
  |                                                                       
  |=================================================                |  75%
  |                                                                       
  |=================================================                |  76%
  |                                                                       
  |==================================================               |  76%
  |                                                                       
  |==================================================               |  77%
  |                                                                       
  |==================================================               |  78%
  |                                                                       
  |===================================================              |  78%
  |                                                                       
  |===================================================              |  79%
  |                                                                       
  |====================================================             |  79%
  |                                                                       
  |====================================================             |  80%
  |                                                                       
  |====================================================             |  81%
  |                                                                       
  |=====================================================            |  81%
  |                                                                       
  |=====================================================            |  82%
  |                                                                       
  |======================================================           |  82%
  |                                                                       
  |======================================================           |  83%
  |                                                                       
  |======================================================           |  84%
  |                                                                       
  |=======================================================          |  84%
  |                                                                       
  |=======================================================          |  85%
  |                                                                       
  |========================================================         |  86%
  |                                                                       
  |========================================================         |  87%
  |                                                                       
  |=========================================================        |  87%
  |                                                                       
  |=========================================================        |  88%
  |                                                                       
  |==========================================================       |  89%
  |                                                                       
  |==========================================================       |  90%
  |                                                                       
  |===========================================================      |  90%
  |                                                                       
  |===========================================================      |  91%
  |                                                                       
  |============================================================     |  92%
  |                                                                       
  |============================================================     |  93%
  |                                                                       
  |=============================================================    |  93%
  |                                                                       
  |=============================================================    |  94%
  |                                                                       
  |==============================================================   |  95%
  |                                                                       
  |==============================================================   |  96%
  |                                                                       
  |===============================================================  |  96%
  |                                                                       
  |===============================================================  |  97%
  |                                                                       
  |===============================================================  |  98%
  |                                                                       
  |================================================================ |  98%
  |                                                                       
  |================================================================ |  99%
  |                                                                       
  |=================================================================|  99%
  |                                                                       
  |=================================================================| 100%
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## Setting levels: control = 0, case = 1
## The higher the score the better, but our data does not return scores
## read more here: https://github.com/Russel88/DAtest/issues/9
## From the paper - In general, the methods per- form better with paired tests, with higher AUC and lower FPR
summary(mytest)
## Warning in summary.DA(mytest): Best Score is equal to zero!
## You might want to re-run with a higher effectSize or pruned dataset (see preDA)
##                      Method  AUC  FPR  FDR Power Score Score.5% Score.95%
##         MgSeq Feature (msf) 0.59 0.06 0.00  0.00  0.00    -1.00      0.02
##       EdgeR qll - TMM (erq) 0.54 0.11 0.00  0.00  0.00    -1.00      0.01
##               DESeq2 (ds2x) 0.55 0.03 0.00  0.00  0.00    -1.00      0.01
##      EdgeR qll - RLE (erq2) 0.57 0.12 0.00  0.00  0.00    -1.00      0.00
##            LIMMA voom (vli) 0.53 0.07 0.00  0.00  0.00    -1.00      0.00
##         ALDEx2 t-test (adx) 0.46 0.00 0.00  0.00  0.00     0.00      0.00
##         ALDEx2 wilcox (adx) 0.49 0.00 0.00  0.00  0.00     0.00      0.00
##                baySeq (bay) 0.47 0.00 0.00  0.00  0.00     0.00      0.00
##  DESeq2 man. geoMeans (ds2) 0.62 0.02 0.00  0.00  0.00     0.00      0.00
##    EdgeR exact - RLE (ere2) 0.59 0.03 0.00  0.00  0.00     0.00      0.00
##     EdgeR exact - TMM (ere) 0.61 0.03 0.00  0.00  0.00     0.00      0.00
##           LIMMA - ALR (lia) 0.61 0.03 0.00  0.00  0.00     0.00      0.00
##           LIMMA - CLR (lic) 0.59 0.03 0.00  0.00  0.00     0.00      0.00
##             Log LIMMA (lli) 0.52 0.02 0.00  0.00  0.00     0.00      0.00
##          Log LIMMA 2 (lli2) 0.54 0.03 0.00  0.00  0.00     0.00      0.00
##            Log t-test (ltt) 0.49 0.01 0.00  0.00  0.00     0.00      0.00
##          Log t-test2 (ltt2) 0.50 0.01 0.00  0.00  0.00     0.00      0.00
##           Permutation (per) 0.45 0.01 0.00  0.00  0.00     0.00      0.00
##     Quasi-Poisson GLM (qpo) 0.65 0.00 0.00  0.00  0.00     0.00      0.00
##          t-test - ALR (tta) 0.55 0.00 0.00  0.00  0.00     0.00      0.00
##          t-test - CLR (ttc) 0.55 0.02 0.00  0.00  0.00     0.00      0.00
##                t-test (ttt) 0.55 0.00 0.00  0.00  0.00     0.00      0.00
##                Wilcox (wil) 0.50 0.02 0.00  0.00  0.00     0.00      0.00
##          Negbinom GLM (neb) 0.73 0.15 0.68  0.40 -0.59    -0.82     -0.29
##        ZI-Poisson GLM (zpo) 0.71 0.36 0.81  0.70 -0.66    -0.95     -0.46
##           Poisson GLM (poi) 0.71 0.40 0.81  0.70 -0.66    -0.89     -0.46
##         ZI-NegBin GLM (znb) 0.68 0.21 0.76  0.43 -0.68    -0.95     -0.43
##             MgSeq ZIG (zig) 0.69 0.26 0.77  0.47 -0.68    -0.93     -0.49
##                SAMseq (sam) 0.65   NA 0.78  0.10 -0.77    -1.00     -0.66
##   
##  *
##  *
##  *
##  *
##  *
##  *
##  *
##  *
##  *
##  *
##  *
##  *
##  *
##  *
##  *
##  *
##  *
##  *
##  *
##  *
##  *
##  *
##  *
##  *
##  *
##  *
##  *
##  *
##  *
## For our data looks like lia and ds2 look like two good tests to compare
## I generally pick two tests and compare their results to find sig ASVs
## The tests are all called DA.xx to run in DAtest package. For instance lia is DA.lia 

res.lia <- DA.lia(TxODA, predictor = "Type")
res.lia
##     Feature        logFC   AveExpr            t         pval   pval.adj
## 1     ASV10 -1.632808844 -5.250044 -2.013112418 0.0533976397 0.39158269
## 2    ASV100 -0.820570091 -5.450627 -1.479626883 0.1496756291 0.58109362
## 3    ASV103  1.446530629 -4.723249  2.670456821 0.0122476735 0.16166929
## 4    ASV105  0.669871331 -4.955218  1.098763042 0.2808437067 0.81638216
## 5    ASV107 -0.902320528 -5.615289 -1.569819387 0.1272253194 0.58109362
## 6     ASV11 -0.413806474 -4.640989 -0.510410640 0.6135987121 0.98212756
## 7   ASV1107 -0.113203213 -5.761590 -0.209854123 0.8352380625 0.98212756
## 8   ASV1133  0.162445585 -5.643142  0.290693868 0.7733390075 0.98212756
## 9    ASV114  1.692543646 -4.858717  3.085001665 0.0044217756 0.09727906
## 10  ASV1155 -0.407043028 -5.908510 -0.785250246 0.4386285491 0.94916342
## 11  ASV1156 -0.065174371 -5.756952 -0.116520511 0.9080372934 0.98212756
## 12  ASV1180  0.319106950 -5.545435  0.561165257 0.5789639401 0.98212756
## 13    ASV12 -2.706972961 -4.712962 -3.493698893 0.0015390960 0.05079017
## 14   ASV121 -0.263075636 -5.171012 -0.411990566 0.6833534838 0.98212756
## 15   ASV123 -0.715869532 -5.490678 -1.304903294 0.2021104721 0.72104277
## 16  ASV1231  0.006560135 -5.701708  0.012468595 0.9901365120 0.99545319
## 17   ASV124 -0.316444897 -5.477254 -0.509246678 0.6144041793 0.98212756
## 18   ASV132 -0.864241303 -5.527674 -1.505485564 0.1429349919 0.58109362
## 19   ASV133 -0.227866733 -5.377346 -0.364589413 0.7180436229 0.98212756
## 20   ASV135 -0.179762349 -5.290202 -0.284814160 0.7777956769 0.98212756
## 21   ASV137 -0.409975173 -5.204583 -0.668773138 0.5088902842 0.98212756
## 22  ASV1470 -0.196878466 -5.813193 -0.377066518 0.7088491730 0.98212756
## 23    ASV15 -0.723989469 -4.910991 -1.019550308 0.3163104574 0.83505961
## 24   ASV151 -0.265950706 -5.319956 -0.436989390 0.6653319475 0.98212756
## 25   ASV158 -0.701557434 -5.506338 -1.222211622 0.2313966684 0.79849104
## 26   ASV159  0.909021523 -5.159962  1.493923153 0.1459181028 0.58109362
## 27   ASV167 -0.116962308 -5.303515 -0.183903764 0.8553593950 0.98212756
## 28   ASV170  0.131710638 -5.484225  0.219582406 0.8277233331 0.98212756
## 29   ASV174 -0.845217864 -5.425090 -1.405198047 0.1705067823 0.64305415
## 30   ASV178 -0.190624034 -5.382575 -0.303204570 0.7638825092 0.98212756
## 31   ASV183 -0.139628767 -5.457372 -0.249511360 0.8047111694 0.98212756
## 32   ASV190 -0.884890153 -5.624004 -1.630351452 0.1137624566 0.58109362
## 33   ASV192  0.959395543 -5.009484  1.604166975 0.1194341849 0.58109362
## 34   ASV193  1.460615076 -4.974681  2.610650998 0.0141138662 0.16936639
## 35   ASV194 -0.305286425 -5.636348 -0.572399528 0.5714300843 0.98212756
## 36   ASV196  0.223474967 -5.371968  0.358768522 0.7223479131 0.98212756
## 37   ASV199 -0.105125400 -5.368408 -0.184716677 0.8547275012 0.98212756
## 38    ASV20 -2.542932717 -4.794982 -3.647476434 0.0010240861 0.04931628
## 39   ASV201 -0.044398385 -5.468714 -0.073923532 0.9415750369 0.98641194
## 40   ASV203  0.062087648 -5.452661  0.107452734 0.9151643158 0.98212756
## 41   ASV209  0.049134180 -5.459138  0.084196708 0.9334743129 0.98641194
## 42   ASV210  0.605507159 -5.296476  1.036862786 0.3083056315 0.83053762
## 43   ASV215  1.096904313 -5.166302  1.765517761 0.0879273751 0.51310614
## 44   ASV219 -0.421874410 -5.479827 -0.725837446 0.4737130879 0.98111923
## 45    ASV22  0.101041291 -4.009873  0.124310970 0.9019203991 0.98212756
## 46   ASV223  0.588245160 -5.429294  1.050249484 0.3022133889 0.83053762
## 47   ASV232  0.114011711 -5.474646  0.196504619 0.8455757183 0.98212756
## 48   ASV238 -0.342136677 -5.673202 -0.615613579 0.5429158604 0.98212756
## 49   ASV241 -1.268674597 -5.444411 -2.091847222 0.0452523382 0.37333179
## 50   ASV242 -0.576135496 -5.680153 -1.048626078 0.3029476755 0.83053762
## 51   ASV245  0.014859829 -5.408698  0.025760640 0.9796234050 0.99545319
## 52   ASV248  0.402072186 -5.503952  0.686427893 0.4978553101 0.98212756
## 53   ASV250  0.191545240 -5.435880  0.337235726 0.7383499766 0.98212756
## 54   ASV253  0.218592389 -5.427833  0.390573243 0.6989460889 0.98212756
## 55   ASV256 -0.049459831 -5.508435 -0.076496568 0.9395454854 0.98641194
## 56    ASV26 -1.615911291 -4.968737 -2.251091770 0.0320698778 0.29631344
## 57   ASV260  0.494793538 -5.457592  0.842489215 0.4063582754 0.94916342
## 58   ASV264  0.279139891 -5.459660  0.467468592 0.6436326415 0.98212756
## 59   ASV267  0.561856262 -5.424060  0.990445757 0.3300885577 0.85434686
## 60   ASV268  0.411289934 -5.326007  0.666793145 0.5101362242 0.98212756
## 61   ASV278  0.714891732 -5.347543  1.180732904 0.2472321625 0.80146213
## 62    ASV28 -1.979534445 -5.076682 -2.774046579 0.0095488685 0.14005007
## 63   ASV281  1.055720711 -5.177128  1.755472651 0.0896597155 0.51310614
## 64    ASV29 -0.105824430 -5.023175 -0.136958564 0.8920029906 0.98212756
## 65    ASV30 -0.817665897 -4.368860 -1.098080771 0.2811365701 0.81638216
## 66   ASV301  0.871115255 -5.269431  1.535682605 0.1353759501 0.58109362
## 67   ASV302  1.136296718 -5.136840  1.941140210 0.0619425195 0.40294284
## 68   ASV303  0.061942189 -5.703160  0.114981328 0.9092465167 0.98212756
## 69   ASV309  0.113762495 -5.648107  0.209795943 0.8352830529 0.98212756
## 70    ASV31 -2.024521878 -5.070175 -2.489689475 0.0187194708 0.19007463
## 71   ASV319  0.224657124 -5.419324  0.399156516 0.6926806218 0.98212756
## 72   ASV326 -0.103490698 -5.588874 -0.194186420 0.8473738069 0.98212756
## 73   ASV331  0.262925606 -5.400189  0.443533969 0.6606468449 0.98212756
## 74   ASV332  0.482188217 -5.473660  0.787217269 0.4374944386 0.94916342
## 75    ASV34 -1.960430866 -5.086233 -2.807240192 0.0088093952 0.14005007
## 76   ASV340 -0.626991894 -5.497927 -1.090288601 0.2844968130 0.81638216
## 77   ASV343 -0.401949671 -5.767246 -0.769231714 0.4479301989 0.95365784
## 78   ASV349  0.345150525 -5.532413  0.608417185 0.5476121461 0.98212756
## 79   ASV361 -0.139657995 -5.706863 -0.251439534 0.8032344559 0.98212756
## 80   ASV375  0.460336085 -5.474820  0.851661700 0.4013288981 0.94916342
## 81   ASV376 -0.298166716 -5.699164 -0.528470454 0.6011645642 0.98212756
## 82    ASV38 -1.183516732 -5.474690 -1.971098995 0.0582505938 0.40294284
## 83   ASV381 -0.412899602 -5.637820 -0.722560893 0.4756941700 0.98111923
## 84    ASV40 -1.754505600 -5.189196 -2.826629843 0.0084026840 0.14005007
## 85   ASV403  0.206122971 -5.601927  0.361475885 0.7203447778 0.98212756
## 86   ASV408  0.003163716 -5.603125  0.005747579 0.9954531864 0.99545319
## 87    ASV43 -0.511436995 -4.853339 -0.708266256 0.4843927376 0.98212756
## 88    ASV44 -0.402645296 -5.037193 -0.610702531 0.5461184675 0.98212756
## 89   ASV451  0.723860265 -5.343058  1.311340694 0.1999553498 0.72104277
## 90    ASV47  0.390114379 -5.096543  0.631673518 0.5325119632 0.98212756
## 91   ASV472  0.271361378 -5.569308  0.490240707 0.6276250744 0.98212756
## 92   ASV480  0.100833866 -5.548813  0.187778689 0.8523482200 0.98212756
## 93   ASV482  0.341278007 -5.534350  0.573080530 0.5709749759 0.98212756
## 94   ASV483 -0.699427751 -5.622928 -1.210159482 0.2359178077 0.79849104
## 95   ASV489  0.168249906 -5.620864  0.296286268 0.7691073912 0.98212756
## 96    ASV53 -1.500768314 -5.316065 -2.228892321 0.0336719819 0.29631344
## 97    ASV54  0.809853040 -4.910178  1.145561324 0.2612736983 0.80204949
## 98   ASV562  0.368912040 -5.520532  0.649940770 0.5208084413 0.98212756
## 99   ASV570  0.096750514 -5.666379  0.178149034 0.8598354307 0.98212756
## 100  ASV591  0.654691451 -5.377643  1.158539916 0.2560261235 0.80204949
## 101    ASV6 -2.784822018 -4.205523 -4.022146919 0.0003727774 0.04920662
## 102   ASV61 -0.125589665 -5.077344 -0.182749715 0.8562566279 0.98212756
## 103   ASV62 -1.981886516 -5.075506 -3.328731789 0.0023687795 0.06253578
## 104   ASV65  1.184301655 -5.112838  1.924310782 0.0641045426 0.40294284
## 105  ASV665 -0.426746438 -5.853076 -0.825230569 0.4159281008 0.94916342
## 106  ASV672  0.200862106 -5.604557  0.335812510 0.7394119442 0.98212756
## 107   ASV68  0.908863666 -4.895292  1.564556556 0.1284550829 0.58109362
## 108   ASV69  0.521933793 -4.829866  0.835584188 0.4101703764 0.94916342
## 109   ASV70 -1.539023942 -5.122705 -2.533959412 0.0168932429 0.18582567
## 110   ASV72 -0.907543380 -5.182505 -1.533109318 0.1360071893 0.58109362
## 111  ASV728  0.497632978 -5.456172  0.862199490 0.3955996631 0.94916342
## 112   ASV74  0.007167104 -5.346783  0.009709984 0.9923186757 0.99545319
## 113  ASV759 -0.499236017 -5.646028 -0.925306344 0.3623867851 0.91990492
## 114   ASV76 -1.215389197 -5.458754 -2.027055837 0.0518674124 0.39158269
## 115  ASV762  0.066430999 -5.681539  0.116465026 0.9080808803 0.98212756
## 116  ASV784 -0.012626868 -5.711302 -0.022419345 0.9822658681 0.99545319
## 117    ASV8 -2.940434377 -4.596232 -3.613562420 0.0011208246 0.04931628
## 118  ASV806  0.487576090 -5.461200  0.820577294 0.4185320962 0.94916342
## 119  ASV808  0.058484198 -5.675746  0.108497698 0.9143426254 0.98212756
## 120   ASV81 -0.109069299 -5.307191 -0.187981738 0.8521904944 0.98212756
## 121  ASV819  0.151859797 -5.629059  0.283179561 0.7790360364 0.98212756
## 122  ASV832  0.168932379 -5.620522  0.312290351 0.7570378738 0.98212756
## 123  ASV835 -0.423364829 -5.700865 -0.792358417 0.4345386444 0.94916342
## 124  ASV850  0.171389426 -5.619294  0.305575338 0.7620946292 0.98212756
## 125  ASV851 -0.075151611 -5.752330 -0.141883233 0.8881461006 0.98212756
## 126   ASV87  0.314119750 -5.121595  0.443421658 0.6607271279 0.98212756
## 127  ASV884 -0.032412228 -5.721195 -0.062350553 0.9507082744 0.98813773
## 128   ASV90 -0.962809064 -5.598258 -1.734932719 0.0932920248 0.51310614
## 129   ASV91  1.013671700 -5.092394  1.494072959 0.1458791346 0.58109362
## 130  ASV925 -0.141814883 -5.785662 -0.270402704 0.7887514798 0.98212756
## 131  ASV959 -0.062116681 -5.736047 -0.112204131 0.9114289153 0.98212756
## 132   ASV97  0.819070840 -5.122117  1.176380615 0.2489389935 0.80146213
##              B          ordering            Method  Kingdom
## 1   -4.1792813 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 2   -4.9948198 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 3   -2.9329863 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 4   -5.4455727 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 5   -4.8712542 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 6   -5.8949891 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 7   -5.9998963 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 8   -5.9802249 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 9   -2.0425021 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 10  -5.7241832 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 11  -6.0147241 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 12  -5.8687608 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 13  -1.1071045 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 14  -5.9388832 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 15  -5.2162393 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 16  -6.0212624 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 17  -5.8955620 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 18  -4.9600246 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 19  -5.9567224 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 20  -5.9818689 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 21  -5.8051477 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 22  -5.9522357 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 23  -5.5241345 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 24  -5.9286087 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 25  -5.3124809 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 26  -4.9756462 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 27  -6.0048684 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 28  -5.9978640 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 29  -5.0920855 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 30  -5.9766160 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 31  -5.9910366 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 32  -4.7849069 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 33  -4.8225904 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 34  -3.0555454 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 35  -5.8626269 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 36  -5.9587645 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 37  -6.0047225 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 38  -0.7437481 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 39  -6.0186756 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 40  -6.0157132 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 41  -6.0178843 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 42  -5.5074275 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 43  -4.5825120 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 44  -5.7670416 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 45  -6.0138103 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 46  -5.4943307 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 47  -6.0025357 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 48  -5.8379269 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 49  -4.0427803 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 50  -5.4959272 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 51  -6.0210148 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 52  -5.7936801 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 53  -5.9660353 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 54  -5.9472103 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 55  -6.0184871 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 56  -3.7553400 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 57  -5.6798495 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 58  -5.9152748 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 59  -5.5516325 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 60  -5.8064157 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 61  -5.3586292 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 62  -2.7169438 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 63  -4.5979985 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 64  -6.0122012 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 65  -5.4462724 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 66  -4.9187466 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 67  -4.3006518 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 68  -6.0148976 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 69  -5.9999082 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 70  -3.2982960 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 71  -5.9439259 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 72  -6.0029764 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 73  -5.9258203 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 74  -5.7227090 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 75  -2.6467484 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 76  -5.4542355 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 77  -5.7360565 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 78  -5.8421616 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 79  -5.9905670 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 80  -5.6724694 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 81  -5.8859353 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 82  -4.2505330 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 83  -5.7693110 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 84  -2.6055342 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 85  -5.9578187 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 86  -6.0213221 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 87  -5.7790958 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 88  -5.8408221 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 89  -5.2085129 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 90  -5.8283018 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 91  -5.9047354 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 92  -6.0041674 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 93  -5.8622512 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 94  -5.3260375 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 95  -5.9786304 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 96  -3.7962923 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 97  -5.3966313 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 98  -5.8170612 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 99  -6.0058824 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 100 -5.3827295 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 101  0.1609431 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 102 -6.0050743 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 103 -1.4904587 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 104 -4.3285514 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 105 -5.6935296 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 106 -5.9665001 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 107 -4.8786330 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 108 -5.6853551 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 109 -3.2102714 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 110 -4.9222911 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 111 -5.6638973 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 112 -6.0212922 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 113 -5.6104797 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 114 -4.1553880 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 115 -6.0147304 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 116 -6.0210933 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 117 -0.8243381 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 118 -5.6971720 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 119 -6.0156033 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 120 -6.0041303 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 121 -5.9823200 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 122 -5.9739003 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 123 -5.7188394 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 124 -5.9759151 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 125 -6.0115325 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 126 -5.9258684 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 127 -6.0194440 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 128 -4.6294454 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 129 -4.9754444 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 130 -5.9857569 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 131 -6.0152049 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 132 -5.3633881 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
##                        Phylum               Class
## 1              Proteobacteria Gammaproteobacteria
## 2              Proteobacteria Alphaproteobacteria
## 3              Actinobacteria      Actinobacteria
## 4              Actinobacteria      Actinobacteria
## 5                  Firmicutes             Bacilli
## 6              Proteobacteria Gammaproteobacteria
## 7              Actinobacteria      Actinobacteria
## 8               Acidobacteria  Acidobacteria_Gp16
## 9              Actinobacteria      Actinobacteria
## 10             Proteobacteria Alphaproteobacteria
## 11             Actinobacteria      Actinobacteria
## 12             Actinobacteria      Actinobacteria
## 13  Cyanobacteria/Chloroplast         Chloroplast
## 14             Actinobacteria      Actinobacteria
## 15             Proteobacteria Gammaproteobacteria
## 16             Actinobacteria      Actinobacteria
## 17             Actinobacteria      Actinobacteria
## 18             Actinobacteria      Actinobacteria
## 19                Chloroflexi      Thermomicrobia
## 20             Actinobacteria      Actinobacteria
## 21                 Firmicutes    Erysipelotrichia
## 22                Chloroflexi        Chloroflexia
## 23             Proteobacteria Gammaproteobacteria
## 24             Actinobacteria      Actinobacteria
## 25             Actinobacteria      Actinobacteria
## 26             Actinobacteria      Actinobacteria
## 27                 Firmicutes             Bacilli
## 28             Actinobacteria      Actinobacteria
## 29             Actinobacteria      Actinobacteria
## 30             Actinobacteria      Actinobacteria
## 31             Actinobacteria      Actinobacteria
## 32             Actinobacteria      Actinobacteria
## 33             Actinobacteria      Actinobacteria
## 34             Actinobacteria      Actinobacteria
## 35             Actinobacteria      Actinobacteria
## 36                 Firmicutes    Erysipelotrichia
## 37             Proteobacteria Alphaproteobacteria
## 38             Proteobacteria Gammaproteobacteria
## 39             Actinobacteria      Actinobacteria
## 40                 Firmicutes          Clostridia
## 41             Actinobacteria      Actinobacteria
## 42             Actinobacteria      Actinobacteria
## 43             Actinobacteria      Actinobacteria
## 44             Proteobacteria Alphaproteobacteria
## 45                 Firmicutes             Bacilli
## 46             Proteobacteria Alphaproteobacteria
## 47             Actinobacteria      Actinobacteria
## 48             Actinobacteria      Actinobacteria
## 49             Proteobacteria Alphaproteobacteria
## 50             Proteobacteria Gammaproteobacteria
## 51                 Firmicutes          Clostridia
## 52                 Firmicutes          Clostridia
## 53                 Firmicutes          Clostridia
## 54             Actinobacteria      Actinobacteria
## 55                Chloroflexi      Thermomicrobia
## 56             Actinobacteria      Actinobacteria
## 57             Actinobacteria      Actinobacteria
## 58                 Firmicutes          Clostridia
## 59                 Firmicutes          Clostridia
## 60                 Firmicutes          Clostridia
## 61             Actinobacteria      Actinobacteria
## 62  Cyanobacteria/Chloroplast         Chloroplast
## 63             Actinobacteria      Actinobacteria
## 64                 Firmicutes             Bacilli
## 65             Actinobacteria      Actinobacteria
## 66             Proteobacteria Alphaproteobacteria
## 67             Proteobacteria Alphaproteobacteria
## 68             Actinobacteria      Actinobacteria
## 69             Actinobacteria      Actinobacteria
## 70             Actinobacteria      Actinobacteria
## 71             Proteobacteria Alphaproteobacteria
## 72                 Firmicutes    Erysipelotrichia
## 73             Actinobacteria      Actinobacteria
## 74              Bacteroidetes         Bacteroidia
## 75             Proteobacteria Gammaproteobacteria
## 76             Actinobacteria      Actinobacteria
## 77             Actinobacteria      Actinobacteria
## 78             Actinobacteria      Actinobacteria
## 79             Actinobacteria      Actinobacteria
## 80             Actinobacteria      Actinobacteria
## 81             Proteobacteria  Betaproteobacteria
## 82             Proteobacteria Gammaproteobacteria
## 83                 Firmicutes          Clostridia
## 84             Proteobacteria Gammaproteobacteria
## 85             Proteobacteria Alphaproteobacteria
## 86             Actinobacteria      Actinobacteria
## 87             Actinobacteria      Actinobacteria
## 88             Actinobacteria      Actinobacteria
## 89             Proteobacteria Alphaproteobacteria
## 90             Proteobacteria Gammaproteobacteria
## 91             Actinobacteria      Actinobacteria
## 92                 Firmicutes          Clostridia
## 93             Proteobacteria Alphaproteobacteria
## 94             Actinobacteria      Actinobacteria
## 95             Proteobacteria Alphaproteobacteria
## 96             Proteobacteria Gammaproteobacteria
## 97             Actinobacteria      Actinobacteria
## 98             Proteobacteria Alphaproteobacteria
## 99             Proteobacteria Alphaproteobacteria
## 100            Actinobacteria      Actinobacteria
## 101            Actinobacteria      Actinobacteria
## 102            Actinobacteria      Actinobacteria
## 103                Firmicutes             Bacilli
## 104 Cyanobacteria/Chloroplast         Chloroplast
## 105            Proteobacteria Alphaproteobacteria
## 106               Chloroflexi                <NA>
## 107            Actinobacteria      Actinobacteria
## 108            Actinobacteria      Actinobacteria
## 109            Actinobacteria      Actinobacteria
## 110            Actinobacteria      Actinobacteria
## 111            Actinobacteria      Actinobacteria
## 112            Actinobacteria      Actinobacteria
## 113            Actinobacteria      Actinobacteria
## 114            Proteobacteria Gammaproteobacteria
## 115            Actinobacteria      Actinobacteria
## 116            Actinobacteria      Actinobacteria
## 117            Proteobacteria Gammaproteobacteria
## 118           Verrucomicrobia      Spartobacteria
## 119            Actinobacteria      Actinobacteria
## 120                Firmicutes          Clostridia
## 121             Bacteroidetes         Bacteroidia
## 122            Proteobacteria Alphaproteobacteria
## 123           Verrucomicrobia      Spartobacteria
## 124            Proteobacteria Alphaproteobacteria
## 125            Proteobacteria Alphaproteobacteria
## 126            Proteobacteria Gammaproteobacteria
## 127            Actinobacteria      Actinobacteria
## 128 Cyanobacteria/Chloroplast         Chloroplast
## 129                Firmicutes    Erysipelotrichia
## 130                Firmicutes          Clostridia
## 131            Proteobacteria Alphaproteobacteria
## 132                Firmicutes          Clostridia
##                                  Order               Family
## 1                    Oceanospirillales       Halomonadaceae
## 2                          Rhizobiales  Methylobacteriaceae
## 3                  Solirubrobacterales Solirubrobacteraceae
## 4                      Actinomycetales   Pseudonocardiaceae
## 5                      Lactobacillales    Carnobacteriaceae
## 6                    Enterobacteriales   Enterobacteriaceae
## 7                  Solirubrobacterales                 <NA>
## 8                                 Gp16                 <NA>
## 9                  Solirubrobacterales Solirubrobacteraceae
## 10                         Rhizobiales    Xanthobacteraceae
## 11                 Solirubrobacterales Solirubrobacteraceae
## 12                     Actinomycetales      Nocardioidaceae
## 13                         Chloroplast         Streptophyta
## 14                     Actinomycetales    Microbacteriaceae
## 15                   Enterobacteriales   Enterobacteriaceae
## 16                     Rubrobacterales     Rubrobacteraceae
## 17                     Actinomycetales     Mycobacteriaceae
## 18                     Actinomycetales    Microbacteriaceae
## 19                   Sphaerobacterales   Sphaerobacteraceae
## 20                 Solirubrobacterales Solirubrobacteraceae
## 21                  Erysipelotrichales  Erysipelotrichaceae
## 22                       Kallotenuales       Kallotenuaceae
## 23                   Enterobacteriales   Enterobacteriaceae
## 24                     Actinomycetales     Mycobacteriaceae
## 25                     Actinomycetales      Nocardioidaceae
## 26                     Actinomycetales    Microbacteriaceae
## 27                          Bacillales        Bacillaceae_1
## 28                     Actinomycetales    Microbacteriaceae
## 29                     Actinomycetales    Microbacteriaceae
## 30                     Actinomycetales   Intrasporangiaceae
## 31                     Actinomycetales      Nocardioidaceae
## 32                     Actinomycetales    Microbacteriaceae
## 33                     Rubrobacterales     Rubrobacteraceae
## 34                     Rubrobacterales     Rubrobacteraceae
## 35                     Actinomycetales     Mycobacteriaceae
## 36                  Erysipelotrichales  Erysipelotrichaceae
## 37                         Rhizobiales  Methylobacteriaceae
## 38                     Pseudomonadales     Pseudomonadaceae
## 39                     Actinomycetales      Nocardioidaceae
## 40                       Clostridiales      Lachnospiraceae
## 41                     Actinomycetales      Nocardioidaceae
## 42                 Solirubrobacterales Solirubrobacteraceae
## 43                     Actinomycetales Propionibacteriaceae
## 44                         Rhizobiales  Methylobacteriaceae
## 45                     Lactobacillales      Enterococcaceae
## 46                         Rhizobiales    Bradyrhizobiaceae
## 47                     Actinomycetales      Nocardioidaceae
## 48                     Actinomycetales      Nocardioidaceae
## 49                         Rhizobiales  Methylobacteriaceae
## 50                   Enterobacteriales   Enterobacteriaceae
## 51                       Clostridiales      Ruminococcaceae
## 52                       Clostridiales       Eubacteriaceae
## 53                       Clostridiales      Lachnospiraceae
## 54                          Gaiellales          Gaiellaceae
## 55                   Sphaerobacterales   Sphaerobacteraceae
## 56                     Actinomycetales   Pseudonocardiaceae
## 57                     Actinomycetales   Pseudonocardiaceae
## 58                       Clostridiales      Ruminococcaceae
## 59                       Clostridiales      Lachnospiraceae
## 60                       Clostridiales      Lachnospiraceae
## 61                     Actinomycetales Propionibacteriaceae
## 62                         Chloroplast         Streptophyta
## 63                     Actinomycetales                 <NA>
## 64                     Lactobacillales    Carnobacteriaceae
## 65                 Solirubrobacterales    Patulibacteraceae
## 66  Alphaproteobacteria_incertae_sedis         Geminicoccus
## 67                         Rhizobiales         Rhodobiaceae
## 68                     Actinomycetales    Streptomycetaceae
## 69                                <NA>                 <NA>
## 70                     Actinomycetales Propionibacteriaceae
## 71                         Rhizobiales  Methylobacteriaceae
## 72                  Erysipelotrichales  Erysipelotrichaceae
## 73                 Solirubrobacterales                 <NA>
## 74                       Bacteroidales       Bacteroidaceae
## 75                     Pseudomonadales     Pseudomonadaceae
## 76                     Actinomycetales   Pseudonocardiaceae
## 77                     Actinomycetales     Mycobacteriaceae
## 78                     Actinomycetales    Cellulomonadaceae
## 79                     Actinomycetales   Pseudonocardiaceae
## 80                 Solirubrobacterales    Conexibacteraceae
## 81                     Burkholderiales       Alcaligenaceae
## 82                     Pseudomonadales     Pseudomonadaceae
## 83                       Clostridiales      Ruminococcaceae
## 84                     Pseudomonadales        Moraxellaceae
## 85                         Rhizobiales  Methylobacteriaceae
## 86                     Actinomycetales                 <NA>
## 87                     Actinomycetales   Pseudonocardiaceae
## 88                     Actinomycetales    Microbacteriaceae
## 89                         Rhizobiales  Methylobacteriaceae
## 90                   Enterobacteriales   Enterobacteriaceae
## 91                     Actinomycetales      Kineosporiaceae
## 92                       Clostridiales      Ruminococcaceae
## 93  Alphaproteobacteria_incertae_sedis         Geminicoccus
## 94                     Actinomycetales       Micrococcaceae
## 95                    Rhodospirillales           Reyranella
## 96                     Pseudomonadales        Moraxellaceae
## 97                    Coriobacteriales    Coriobacteriaceae
## 98                         Rhizobiales    Hyphomicrobiaceae
## 99                         Rhizobiales  Methylobacteriaceae
## 100                Solirubrobacterales Solirubrobacteraceae
## 101                    Actinomycetales    Sanguibacteraceae
## 102                    Actinomycetales                 <NA>
## 103                         Bacillales    Staphylococcaceae
## 104                        Chloroplast          Chlorophyta
## 105                   Sphingomonadales    Sphingomonadaceae
## 106                               <NA>                 <NA>
## 107                    Actinomycetales     Mycobacteriaceae
## 108                    Actinomycetales         Nocardiaceae
## 109                    Actinomycetales   Pseudonocardiaceae
## 110                    Actinomycetales   Pseudonocardiaceae
## 111                   Acidimicrobiales    Acidimicrobiaceae
## 112                    Actinomycetales Propionibacteriaceae
## 113                    Actinomycetales Propionibacteriaceae
## 114                    Pseudomonadales     Pseudomonadaceae
## 115                   Acidimicrobiales    Acidimicrobiaceae
## 116                    Actinomycetales   Intrasporangiaceae
## 117                    Pseudomonadales     Pseudomonadaceae
## 118                     Terrimicrobium                 <NA>
## 119                         Gaiellales          Gaiellaceae
## 120                      Clostridiales      Ruminococcaceae
## 121                      Bacteroidales       Bacteroidaceae
## 122 Alphaproteobacteria_incertae_sedis         Geminicoccus
## 123                     Terrimicrobium                 <NA>
## 124                        Rhizobiales    Hyphomicrobiaceae
## 125 Alphaproteobacteria_incertae_sedis         Geminicoccus
## 126                  Enterobacteriales   Enterobacteriaceae
## 127                Solirubrobacterales                 <NA>
## 128                        Chloroplast         Streptophyta
## 129                 Erysipelotrichales  Erysipelotrichaceae
## 130                      Clostridiales      Lachnospiraceae
## 131 Alphaproteobacteria_incertae_sedis         Geminicoccus
## 132                      Clostridiales      Lachnospiraceae
##                 Genus        Species
## 1          Salinicola         socius
## 2    Methylobacterium           <NA>
## 3     Solirubrobacter           <NA>
## 4   Actinomycetospora           <NA>
## 5      Carnobacterium           <NA>
## 6        Buttiauxella           <NA>
## 7                <NA>           <NA>
## 8                <NA>           <NA>
## 9     Solirubrobacter           <NA>
## 10               <NA>           <NA>
## 11    Solirubrobacter           <NA>
## 12       Nocardioides           <NA>
## 13               <NA>           <NA>
## 14         Agrococcus           <NA>
## 15               <NA>           <NA>
## 16        Rubrobacter           <NA>
## 17      Mycobacterium           <NA>
## 18     Curtobacterium           <NA>
## 19               <NA>           <NA>
## 20    Solirubrobacter           <NA>
## 21  Clostridium_XVIII           <NA>
## 22         Kallotenue           <NA>
## 23       Enterobacter           <NA>
## 24      Mycobacterium         JC2972
## 25       Nocardioides           <NA>
## 26     Microbacterium           <NA>
## 27           Bacillus           <NA>
## 28     Curtobacterium           <NA>
## 29     Microbacterium           <NA>
## 30               <NA>           <NA>
## 31       Nocardioides           <NA>
## 32  Pseudoclavibacter       helvolus
## 33        Rubrobacter           <NA>
## 34        Rubrobacter           <NA>
## 35      Mycobacterium           <NA>
## 36  Clostridium_XVIII           <NA>
## 37               <NA>           <NA>
## 38        Pseudomonas           <NA>
## 39       Nocardioides           <NA>
## 40               <NA>           <NA>
## 41       Nocardioides    ginsengagri
## 42    Solirubrobacter           <NA>
## 43       Microlunatus           <NA>
## 44               <NA>           <NA>
## 45       Enterococcus           <NA>
## 46     Bradyrhizobium           <NA>
## 47       Nocardioides           <NA>
## 48       Nocardioides           <NA>
## 49   Methylobacterium           <NA>
## 50            Pantoea           <NA>
## 51     Intestinimonas           <NA>
## 52       Anaerofustis           <NA>
## 53               <NA>           <NA>
## 54            Gaiella           <NA>
## 55      Sphaerobacter           <NA>
## 56  Actinomycetospora           <NA>
## 57     Pseudonocardia           <NA>
## 58               <NA>           <NA>
## 59   Clostridium_XlVa           <NA>
## 60               <NA>           <NA>
## 61       Microlunatus           <NA>
## 62               <NA>           <NA>
## 63               <NA>           <NA>
## 64      Catellicoccus           <NA>
## 65       Patulibacter   minatonensis
## 66               <NA>           <NA>
## 67               <NA>           <NA>
## 68       Streptomyces           <NA>
## 69               <NA>           <NA>
## 70     Friedmanniella           <NA>
## 71         Microvirga     zambiensis
## 72  Clostridium_XVIII           <NA>
## 73               <NA>           <NA>
## 74        Bacteroides           <NA>
## 75        Pseudomonas           <NA>
## 76     Pseudonocardia           <NA>
## 77      Mycobacterium           <NA>
## 78       Cellulomonas           <NA>
## 79     Pseudonocardia           <NA>
## 80       Conexibacter           <NA>
## 81      Achromobacter           <NA>
## 82        Pseudomonas           <NA>
## 83        Anaerofilum           <NA>
## 84      Acinetobacter           <NA>
## 85         Microvirga           <NA>
## 86               <NA>           <NA>
## 87     Pseudonocardia    endophytica
## 88     Microbacterium           <NA>
## 89         Microvirga           <NA>
## 90            Pantoea           <NA>
## 91  Pseudokineococcus           <NA>
## 92     Clostridium_IV           <NA>
## 93               <NA>           <NA>
## 94       Arthrobacter           <NA>
## 95               <NA>           <NA>
## 96      Acinetobacter           <NA>
## 97   Denitrobacterium           <NA>
## 98        Rhodoplanes           <NA>
## 99         Microvirga    lotononidis
## 100   Solirubrobacter           <NA>
## 101      Sanguibacter           <NA>
## 102              <NA>           <NA>
## 103    Staphylococcus           <NA>
## 104              <NA>           <NA>
## 105      Sphingopyxis           <NA>
## 106              <NA>           <NA>
## 107     Mycobacterium           <NA>
## 108       Rhodococcus           <NA>
## 109 Actinomycetospora chiangmaiensis
## 110 Actinomycetospora           <NA>
## 111     Ilumatobacter           <NA>
## 112              <NA>           <NA>
## 113    Friedmanniella           <NA>
## 114       Pseudomonas           <NA>
## 115     Ilumatobacter           <NA>
## 116        Janibacter           <NA>
## 117       Pseudomonas           <NA>
## 118              <NA>           <NA>
## 119           Gaiella           <NA>
## 120    Intestinimonas           <NA>
## 121       Bacteroides           <NA>
## 122              <NA>           <NA>
## 123              <NA>           <NA>
## 124     Pedomicrobium           <NA>
## 125              <NA>           <NA>
## 126           Pantoea           <NA>
## 127              <NA>           <NA>
## 128              <NA>           <NA>
## 129 Clostridium_XVIII           <NA>
## 130  Clostridium_XlVa           <NA>
## 131              <NA>           <NA>
## 132              <NA>           <NA>
res.lia[res.lia$pval.adj < 0.05,"Feature"]
## [1] "ASV20" "ASV6"  "ASV8"
## Three ASVs sig: ASV20, ASV6 and ASV8

res.ds2 <- DA.ds2(TxODA, predictor = "Type")
## converting counts to integer mode
## using pre-existing size factors
## estimating dispersions
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates
## fitting model and testing
res.ds2
##     Feature    baseMean log2FoldChange    lfcSE         stat         pval
## 1     ASV10  34.2179534  -23.375001965 2.729266 -8.564574290           NA
## 2    ASV100   1.9243463   -1.980434888 2.207519 -0.897131439 0.3696487845
## 3    ASV103   5.3539615    2.987449711 1.783761  1.674803793 0.0939727344
## 4    ASV105   3.4747901    2.078751667 1.812523  1.146883186 0.2514299027
## 5    ASV107   1.2037348   -3.623599875 2.304323 -1.572522290 0.1158294740
## 6     ASV11  43.3719283    3.225699429 2.231007  1.445848809           NA
## 7   ASV1107   0.5888269    2.721708335 2.372118  1.147374691 0.2512267965
## 8   ASV1133   0.9780784    2.513092593 2.559302  0.981944548 0.3261271674
## 9    ASV114   4.4221562    5.626583871 1.780849  3.159495246 0.0015804268
## 10  ASV1155   0.3186708    1.681392613 2.766583  0.607750565 0.5433529208
## 11  ASV1156   0.6269299    1.626876030 2.625114  0.619735308 0.5354320658
## 12  ASV1180   1.1251168    3.638620415 2.474303  1.470564091 0.1414090411
## 13    ASV12  26.6414817   -8.139802299 2.362738 -3.445072208 0.0005709069
## 14   ASV121   2.8460418    0.103859064 2.199885  0.047211127 0.9623449597
## 15   ASV123   1.7101913   -1.861123788 2.587129 -0.719378128 0.4719079692
## 16  ASV1231   0.6533466    2.841119957 2.549672  1.114308078 0.2651470426
## 17   ASV124   1.8182171    0.500798337 2.605439  0.192212651 0.8475756362
## 18   ASV132   1.3810911   -2.712049689 2.556477 -1.060854124 0.2887562009
## 19   ASV133   3.0391495   -0.634819789 2.644490 -0.240053729 0.8102886043
## 20   ASV135   1.9416786    0.414403210 2.352979  0.176118540 0.8602008157
## 21   ASV137   2.7023639    0.553801245 2.200846  0.251631075 0.8013262367
## 22  ASV1470   0.4763546    1.479419090 2.662416  0.555667830 0.5784379527
## 23    ASV15   9.6832666   -1.704645528 2.341745 -0.727938054           NA
## 24   ASV151   2.0130301    0.005002347 2.024228  0.002471237 0.9980282404
## 25   ASV158   1.5948986   -2.245101421 2.385886 -0.940992554 0.3467086751
## 26   ASV159   3.2284607    3.331136513 1.978387  1.683763589 0.0922273666
## 27   ASV167   1.7389911    0.853275387 2.150129  0.396848497 0.6914791858
## 28   ASV170   1.7127238    1.682631416 2.201323  0.764372882 0.4446450646
## 29   ASV174   1.3916588   -1.301793449 2.002727 -0.650010497 0.5156854414
## 30   ASV178   3.0491960   -0.141002407 2.456425 -0.057401477 0.9542253868
## 31   ASV183   2.0528914   -0.571352108 2.228422 -0.256393128 0.7976472936
## 32   ASV190   0.7991581   -3.094147115 2.524835 -1.225485061 0.2203925153
## 33   ASV192   3.3183006    3.403896121 1.923860  1.769305148 0.0768429648
## 34   ASV193   3.9222150    5.453097509 1.816361  3.002210501 0.0026802677
## 35   ASV194   0.9664851   -0.112895232 2.609940 -0.043255880 0.9654975607
## 36   ASV196   2.5883061    2.054750821 2.591894  0.792760363 0.4279174542
## 37   ASV199   1.6547881    0.791563281 1.851247  0.427583935 0.6689540642
## 38    ASV20   8.5750594   -6.511677066 1.893844 -3.438338673 0.0005852952
## 39   ASV201   1.3682115    0.311485651 2.575321  0.120950244 0.9037304454
## 40   ASV203   1.5341570    1.054688490 2.571619  0.410126304 0.6817132983
## 41   ASV209   1.4051792    0.875257668 2.359278  0.370985402 0.7106484043
## 42   ASV210   2.9070939    3.718627978 2.333867  1.593333524 0.1110853899
## 43   ASV215   3.3187126    4.652758793 2.078267  2.238769077 0.0251709453
## 44   ASV219   1.5896668   -0.308274939 2.390172 -0.128976028 0.8973766169
## 45    ASV22  19.4604625    0.581493874 1.867965  0.311298116 0.7555739992
## 46   ASV223   1.6052772    3.579071628 1.929883  1.854553840 0.0636599650
## 47   ASV232   1.6335508    1.706242848 2.572862  0.663169224 0.5072221795
## 48   ASV238   0.7267150   -0.487203838 2.631183 -0.185165329 0.8530993621
## 49   ASV241   1.1264070   -3.011513357 2.278219 -1.321871522 0.1862109368
## 50   ASV242   0.8063944   -1.623582462 2.608530 -0.622412844 0.5336704369
## 51   ASV245   2.4705398    1.250423625 2.416253  0.517505191 0.6048035465
## 52   ASV248   1.5780633    4.141046986 2.474776  1.673301925 0.0942678736
## 53   ASV250   2.2779902    2.312057181 2.386021  0.969001268 0.3325445566
## 54   ASV253   1.2458464    2.179071917 2.131742  1.022202417 0.3066851069
## 55   ASV256   2.7020863    2.130374762 2.640018  0.806954703           NA
## 56    ASV26  11.3001751   -4.551338105 2.273280 -2.002102161 0.0452737451
## 57   ASV260   1.3269234    3.897495370 2.448681  1.591671080 0.1114586297
## 58   ASV264   3.2166297    3.858418769 2.594046  1.487413238 0.1369057026
## 59   ASV267   1.8742603    4.388044337 2.455007  1.787385804 0.0738751544
## 60   ASV268   2.0094891    2.116561325 2.337842  0.905348400 0.3652808430
## 61   ASV278   2.9175376    5.022850854 2.467478  2.035621215 0.0417884058
## 62    ASV28   7.9703221   -6.403146675 2.502961 -2.558228707 0.0105206874
## 63   ASV281   3.4419600    5.266180705 2.223621  2.368290763 0.0178704853
## 64    ASV29   8.5655036   -0.597561943 2.740627 -0.218038428 0.8273991706
## 65    ASV30  11.0742620   -1.667642893 1.669526 -0.998872028 0.3178566880
## 66   ASV301   2.7029854    4.906762407 1.892216  2.593130457 0.0095106687
## 67   ASV302   3.0536784    5.093220720 1.851928  2.750226007 0.0059554173
## 68   ASV303   1.4661180    2.414194495 2.256361  1.069950356 0.2846416552
## 69   ASV309   1.0173908    3.481714163 2.304549  1.510800856 0.1308391966
## 70    ASV31  10.4574322   -6.306721966 2.224485 -2.835137439 0.0045805975
## 71   ASV319   1.5601456    1.677207881 2.160225  0.776404198 0.4375103668
## 72   ASV326   0.9499856    1.690625278 2.581445  0.654914294 0.5125229369
## 73   ASV331   1.5678448    1.659280248 2.339299  0.709306696 0.4781341743
## 74   ASV332   2.4373628    4.180800746 2.531835  1.651292625 0.0986788375
## 75    ASV34   6.1251341   -6.021980085 2.473523 -2.434576550 0.0149092259
## 76   ASV340   1.0854008   -0.559391354 2.576636 -0.217101389 0.8281293318
## 77   ASV343   0.9424039   -1.695069609 2.419218 -0.700668325 0.4835100280
## 78   ASV349   1.1652047    3.705260749 2.472000  1.498891745 0.1339017182
## 79   ASV361   1.1725349   -0.293915504 2.435883 -0.120660744 0.9039597532
## 80   ASV375   1.7562221    4.283577118 2.264518  1.891606748 0.0585433962
## 81   ASV376   0.5877378   -0.767587920 2.671627 -0.287311053 0.7738741601
## 82    ASV38   1.9176015   -4.351674104 2.486534 -1.750096394 0.0801016819
## 83   ASV381   0.7693847   -0.667126378 2.625505 -0.254094453 0.7994225883
## 84    ASV40   4.3783658   -5.534606661 2.269305 -2.438899652 0.0147320585
## 85   ASV403   0.8812682    3.311839918 2.289147  1.446756962 0.1479650046
## 86   ASV408   0.8888009    2.049448880 2.343074  0.874683649 0.3817460592
## 87    ASV43   6.2137549   -0.886919627 1.956411 -0.453340029 0.6503039131
## 88    ASV44   3.3394319    0.303105717 2.024614  0.149710382 0.8809931166
## 89   ASV451   1.9552970    4.439169701 2.037761  2.178454040 0.0293722504
## 90    ASV47   4.2840602    1.947045772 2.059235  0.945518797 0.3443940788
## 91   ASV472   1.0590712    3.569590417 2.485346  1.436254632 0.1509298985
## 92   ASV480   1.2892998    2.357206900 2.554772  0.922668132 0.3561801783
## 93   ASV482   1.3074387    3.885923703 2.275922  1.707406365 0.0877465481
## 94   ASV483   0.7241087   -1.428966935 2.629868 -0.543360655 0.5868815098
## 95   ASV489   1.0685228    3.572844392 2.507164  1.425053982 0.1541415974
## 96    ASV53   2.4411203   -4.715794202 2.452644 -1.922738774 0.0545128647
## 97    ASV54  15.1370435    3.355011246 2.535507  1.323210951 0.1857652354
## 98   ASV562   1.4104736    3.979752680 2.474764  1.608133927 0.1078058502
## 99   ASV570   1.1214608    2.960702564 2.551152  1.160535706 0.2458307652
## 100  ASV591   1.5948867    4.157289295 2.217518  1.874748860 0.0608272817
## 101    ASV6  19.4001034   -3.432976187 1.915173 -1.792514659 0.0730505632
## 102   ASV61   7.3848880   -0.114002993 2.534717 -0.044976614 0.9641259495
## 103   ASV62   4.6964277   -5.641844783 2.063417 -2.734224483 0.0062527399
## 104   ASV65   6.9687195    6.278158640 2.126917  2.951764556           NA
## 105  ASV665   0.2464120   -1.541006122 2.828192 -0.544873164 0.5858407542
## 106  ASV672   0.9700731    3.454209411 2.504077  1.379434387 0.1677608632
## 107   ASV68   5.2525932    1.142204714 1.789392  0.638320123 0.5232653151
## 108   ASV69   5.4043550    0.696302532 1.783815  0.390344511 0.6962818132
## 109   ASV70   2.7059538   -3.284091792 2.116851 -1.551404667 0.1208047375
## 110   ASV72   4.0169363   -2.090461325 2.063151 -1.013237366 0.3109467966
## 111  ASV728   1.4884839    4.067325575 2.249586  1.808032571 0.0706014314
## 112   ASV74   8.2967377    2.218387851 2.584731  0.858266366           NA
## 113  ASV759   0.6433571   -0.244263542 2.628376 -0.092933267 0.9259565770
## 114   ASV76   1.4942066   -3.989159326 2.260899 -1.764412903 0.0776624874
## 115  ASV762   0.6224476    2.023497994 2.581300  0.783906586 0.4330949250
## 116  ASV784   0.5686328    2.690566453 2.576496  1.044273673 0.2963587899
## 117    ASV8  21.7998701   -7.853093621 2.298720 -3.416290287 0.0006348054
## 118  ASV806   1.3008334    3.870455733 2.449936  1.579819268 0.1141482619
## 119  ASV808   0.9912038    3.461890811 2.527194  1.369855812 0.1707319157
## 120   ASV81   3.4929768   -0.379204006 2.452329 -0.154630151 0.8771128988
## 121  ASV819   1.0190138    3.509355035 2.509767  1.398279271 0.1620292203
## 122  ASV832   0.7463130    3.070216536 2.295965  1.337222548 0.1811500040
## 123  ASV835   0.5664146    0.249003648 2.663081  0.093502078 0.9255046989
## 124  ASV850   0.6881852    2.960140502 2.518902  1.175171095 0.2399262718
## 125  ASV851   0.5498898    1.743764888 2.617285  0.666249482 0.5052516496
## 126   ASV87   6.1096627    3.029116449 2.434907  1.244037807 0.2134856489
## 127  ASV884   0.6413848    2.831783559 2.564283  1.104318046 0.2694551973
## 128   ASV90   0.6913735   -2.289599735 2.562871 -0.893372951 0.3716574830
## 129   ASV91   6.8622206    5.032678927 2.375147  2.118891359 0.0340996494
## 130  ASV925   0.6260716    1.951085798 2.616211  0.745767656 0.4558077815
## 131  ASV959   0.5479861    2.641157375 2.370463  1.114194935 0.2651955678
## 132   ASV97   6.5294084    4.004002124 2.407971  1.662811391 0.0963501957
## 133  Others 622.4605134   -0.295635066 1.237784 -0.238842256 0.8112279027
##              ordering   pval.adj                     Method  Kingdom
## 1   CloacalSwab>Fecal         NA DESeq2 man. geoMeans (ds2) Bacteria
## 2   CloacalSwab>Fecal 0.62105921 DESeq2 man. geoMeans (ds2) Bacteria
## 3   Fecal>CloacalSwab 0.36859448 DESeq2 man. geoMeans (ds2) Bacteria
## 4   Fecal>CloacalSwab 0.54121352 DESeq2 man. geoMeans (ds2) Bacteria
## 5   CloacalSwab>Fecal 0.37718829 DESeq2 man. geoMeans (ds2) Bacteria
## 6   Fecal>CloacalSwab         NA DESeq2 man. geoMeans (ds2) Bacteria
## 7   Fecal>CloacalSwab 0.54121352 DESeq2 man. geoMeans (ds2) Bacteria
## 8   Fecal>CloacalSwab 0.60026305 DESeq2 man. geoMeans (ds2) Bacteria
## 9   Fecal>CloacalSwab 0.05017855 DESeq2 man. geoMeans (ds2) Bacteria
## 10  Fecal>CloacalSwab 0.74199807 DESeq2 man. geoMeans (ds2) Bacteria
## 11  Fecal>CloacalSwab 0.73912905 DESeq2 man. geoMeans (ds2) Bacteria
## 12  Fecal>CloacalSwab 0.40815791 DESeq2 man. geoMeans (ds2) Bacteria
## 13  CloacalSwab>Fecal 0.02687343 DESeq2 man. geoMeans (ds2) Bacteria
## 14  Fecal>CloacalSwab 0.97316024 DESeq2 man. geoMeans (ds2) Bacteria
## 15  CloacalSwab>Fecal 0.72207605 DESeq2 man. geoMeans (ds2) Bacteria
## 16  Fecal>CloacalSwab 0.55194855 DESeq2 man. geoMeans (ds2) Bacteria
## 17  Fecal>CloacalSwab 0.94996090 DESeq2 man. geoMeans (ds2) Bacteria
## 18  CloacalSwab>Fecal 0.57300059 DESeq2 man. geoMeans (ds2) Bacteria
## 19  CloacalSwab>Fecal 0.93659949 DESeq2 man. geoMeans (ds2) Bacteria
## 20  Fecal>CloacalSwab 0.94996090 DESeq2 man. geoMeans (ds2) Bacteria
## 21  Fecal>CloacalSwab 0.93659949 DESeq2 man. geoMeans (ds2) Bacteria
## 22  Fecal>CloacalSwab 0.77639533 DESeq2 man. geoMeans (ds2) Bacteria
## 23  CloacalSwab>Fecal         NA DESeq2 man. geoMeans (ds2) Bacteria
## 24  Fecal>CloacalSwab 0.99802824 DESeq2 man. geoMeans (ds2) Bacteria
## 25  CloacalSwab>Fecal 0.61155558 DESeq2 man. geoMeans (ds2) Bacteria
## 26  Fecal>CloacalSwab 0.36859448 DESeq2 man. geoMeans (ds2) Bacteria
## 27  Fecal>CloacalSwab 0.86693912 DESeq2 man. geoMeans (ds2) Bacteria
## 28  Fecal>CloacalSwab 0.69715955 DESeq2 man. geoMeans (ds2) Bacteria
## 29  CloacalSwab>Fecal 0.73586574 DESeq2 man. geoMeans (ds2) Bacteria
## 30  CloacalSwab>Fecal 0.97316024 DESeq2 man. geoMeans (ds2) Bacteria
## 31  CloacalSwab>Fecal 0.93659949 DESeq2 man. geoMeans (ds2) Bacteria
## 32  CloacalSwab>Fecal 0.50890635 DESeq2 man. geoMeans (ds2) Bacteria
## 33  Fecal>CloacalSwab 0.36331834 DESeq2 man. geoMeans (ds2) Bacteria
## 34  Fecal>CloacalSwab 0.06807880 DESeq2 man. geoMeans (ds2) Bacteria
## 35  CloacalSwab>Fecal 0.97316024 DESeq2 man. geoMeans (ds2) Bacteria
## 36  Fecal>CloacalSwab 0.69454771 DESeq2 man. geoMeans (ds2) Bacteria
## 37  Fecal>CloacalSwab 0.85815319 DESeq2 man. geoMeans (ds2) Bacteria
## 38  CloacalSwab>Fecal 0.02687343 DESeq2 man. geoMeans (ds2) Bacteria
## 39  Fecal>CloacalSwab 0.95669074 DESeq2 man. geoMeans (ds2) Bacteria
## 40  Fecal>CloacalSwab 0.86577589 DESeq2 man. geoMeans (ds2) Bacteria
## 41  Fecal>CloacalSwab 0.87623638 DESeq2 man. geoMeans (ds2) Bacteria
## 42  Fecal>CloacalSwab 0.37718829 DESeq2 man. geoMeans (ds2) Bacteria
## 43  Fecal>CloacalSwab 0.22833643 DESeq2 man. geoMeans (ds2) Bacteria
## 44  CloacalSwab>Fecal 0.95669074 DESeq2 man. geoMeans (ds2) Bacteria
## 45  Fecal>CloacalSwab 0.92267210 DESeq2 man. geoMeans (ds2) Bacteria
## 46  Fecal>CloacalSwab 0.36331834 DESeq2 man. geoMeans (ds2) Bacteria
## 47  Fecal>CloacalSwab 0.73586574 DESeq2 man. geoMeans (ds2) Bacteria
## 48  CloacalSwab>Fecal 0.94996090 DESeq2 man. geoMeans (ds2) Bacteria
## 49  CloacalSwab>Fecal 0.44620357 DESeq2 man. geoMeans (ds2) Bacteria
## 50  CloacalSwab>Fecal 0.73912905 DESeq2 man. geoMeans (ds2) Bacteria
## 51  Fecal>CloacalSwab 0.79185619 DESeq2 man. geoMeans (ds2) Bacteria
## 52  Fecal>CloacalSwab 0.36859448 DESeq2 man. geoMeans (ds2) Bacteria
## 53  Fecal>CloacalSwab 0.60333084 DESeq2 man. geoMeans (ds2) Bacteria
## 54  Fecal>CloacalSwab 0.58940661 DESeq2 man. geoMeans (ds2) Bacteria
## 55  Fecal>CloacalSwab         NA DESeq2 man. geoMeans (ds2) Bacteria
## 56  CloacalSwab>Fecal 0.31943142 DESeq2 man. geoMeans (ds2) Bacteria
## 57  Fecal>CloacalSwab 0.37718829 DESeq2 man. geoMeans (ds2) Bacteria
## 58  Fecal>CloacalSwab 0.40434940 DESeq2 man. geoMeans (ds2) Bacteria
## 59  Fecal>CloacalSwab 0.36331834 DESeq2 man. geoMeans (ds2) Bacteria
## 60  Fecal>CloacalSwab 0.62105921 DESeq2 man. geoMeans (ds2) Bacteria
## 61  Fecal>CloacalSwab 0.31218397 DESeq2 man. geoMeans (ds2) Bacteria
## 62  CloacalSwab>Fecal 0.13361273 DESeq2 man. geoMeans (ds2) Bacteria
## 63  Fecal>CloacalSwab 0.17458090 DESeq2 man. geoMeans (ds2) Bacteria
## 64  CloacalSwab>Fecal 0.93903951 DESeq2 man. geoMeans (ds2) Bacteria
## 65  CloacalSwab>Fecal 0.59364411 DESeq2 man. geoMeans (ds2) Bacteria
## 66  Fecal>CloacalSwab 0.13361273 DESeq2 man. geoMeans (ds2) Bacteria
## 67  Fecal>CloacalSwab 0.09926225 DESeq2 man. geoMeans (ds2) Bacteria
## 68  Fecal>CloacalSwab 0.57300059 DESeq2 man. geoMeans (ds2) Bacteria
## 69  Fecal>CloacalSwab 0.40434940 DESeq2 man. geoMeans (ds2) Bacteria
## 70  CloacalSwab>Fecal 0.09695598 DESeq2 man. geoMeans (ds2) Bacteria
## 71  Fecal>CloacalSwab 0.69454771 DESeq2 man. geoMeans (ds2) Bacteria
## 72  Fecal>CloacalSwab 0.73586574 DESeq2 man. geoMeans (ds2) Bacteria
## 73  Fecal>CloacalSwab 0.72242087 DESeq2 man. geoMeans (ds2) Bacteria
## 74  Fecal>CloacalSwab 0.36859448 DESeq2 man. geoMeans (ds2) Bacteria
## 75  CloacalSwab>Fecal 0.15778931 DESeq2 man. geoMeans (ds2) Bacteria
## 76  CloacalSwab>Fecal 0.93903951 DESeq2 man. geoMeans (ds2) Bacteria
## 77  CloacalSwab>Fecal 0.72242087 DESeq2 man. geoMeans (ds2) Bacteria
## 78  Fecal>CloacalSwab 0.40434940 DESeq2 man. geoMeans (ds2) Bacteria
## 79  CloacalSwab>Fecal 0.95669074 DESeq2 man. geoMeans (ds2) Bacteria
## 80  Fecal>CloacalSwab 0.36331834 DESeq2 man. geoMeans (ds2) Bacteria
## 81  CloacalSwab>Fecal 0.93601922 DESeq2 man. geoMeans (ds2) Bacteria
## 82  CloacalSwab>Fecal 0.36331834 DESeq2 man. geoMeans (ds2) Bacteria
## 83  CloacalSwab>Fecal 0.93659949 DESeq2 man. geoMeans (ds2) Bacteria
## 84  CloacalSwab>Fecal 0.15778931 DESeq2 man. geoMeans (ds2) Bacteria
## 85  Fecal>CloacalSwab 0.41651027 DESeq2 man. geoMeans (ds2) Bacteria
## 86  Fecal>CloacalSwab 0.62963311 DESeq2 man. geoMeans (ds2) Bacteria
## 87  CloacalSwab>Fecal 0.84274079 DESeq2 man. geoMeans (ds2) Bacteria
## 88  Fecal>CloacalSwab 0.95629167 DESeq2 man. geoMeans (ds2) Bacteria
## 89  Fecal>CloacalSwab 0.24868505 DESeq2 man. geoMeans (ds2) Bacteria
## 90  Fecal>CloacalSwab 0.61155558 DESeq2 man. geoMeans (ds2) Bacteria
## 91  Fecal>CloacalSwab 0.41651027 DESeq2 man. geoMeans (ds2) Bacteria
## 92  Fecal>CloacalSwab 0.61965593 DESeq2 man. geoMeans (ds2) Bacteria
## 93  Fecal>CloacalSwab 0.36859448 DESeq2 man. geoMeans (ds2) Bacteria
## 94  CloacalSwab>Fecal 0.77639533 DESeq2 man. geoMeans (ds2) Bacteria
## 95  Fecal>CloacalSwab 0.41651027 DESeq2 man. geoMeans (ds2) Bacteria
## 96  CloacalSwab>Fecal 0.36331834 DESeq2 man. geoMeans (ds2) Bacteria
## 97  Fecal>CloacalSwab 0.44620357 DESeq2 man. geoMeans (ds2) Bacteria
## 98  Fecal>CloacalSwab 0.37718829 DESeq2 man. geoMeans (ds2) Bacteria
## 99  Fecal>CloacalSwab 0.54121352 DESeq2 man. geoMeans (ds2) Bacteria
## 100 Fecal>CloacalSwab 0.36331834 DESeq2 man. geoMeans (ds2) Bacteria
## 101 CloacalSwab>Fecal 0.36331834 DESeq2 man. geoMeans (ds2) Bacteria
## 102 CloacalSwab>Fecal 0.97316024 DESeq2 man. geoMeans (ds2) Bacteria
## 103 CloacalSwab>Fecal 0.09926225 DESeq2 man. geoMeans (ds2) Bacteria
## 104 Fecal>CloacalSwab         NA DESeq2 man. geoMeans (ds2) Bacteria
## 105 CloacalSwab>Fecal 0.77639533 DESeq2 man. geoMeans (ds2) Bacteria
## 106 Fecal>CloacalSwab 0.43365907 DESeq2 man. geoMeans (ds2) Bacteria
## 107 Fecal>CloacalSwab 0.73838550 DESeq2 man. geoMeans (ds2) Bacteria
## 108 Fecal>CloacalSwab 0.86693912 DESeq2 man. geoMeans (ds2) Bacteria
## 109 CloacalSwab>Fecal 0.38355504 DESeq2 man. geoMeans (ds2) Bacteria
## 110 CloacalSwab>Fecal 0.58940661 DESeq2 man. geoMeans (ds2) Bacteria
## 111 Fecal>CloacalSwab 0.36331834 DESeq2 man. geoMeans (ds2) Bacteria
## 112 Fecal>CloacalSwab         NA DESeq2 man. geoMeans (ds2) Bacteria
## 113 CloacalSwab>Fecal 0.96390562 DESeq2 man. geoMeans (ds2) Bacteria
## 114 CloacalSwab>Fecal 0.36331834 DESeq2 man. geoMeans (ds2) Bacteria
## 115 Fecal>CloacalSwab 0.69454771 DESeq2 man. geoMeans (ds2) Bacteria
## 116 Fecal>CloacalSwab 0.57903948 DESeq2 man. geoMeans (ds2) Bacteria
## 117 CloacalSwab>Fecal 0.02687343 DESeq2 man. geoMeans (ds2) Bacteria
## 118 Fecal>CloacalSwab 0.37718829 DESeq2 man. geoMeans (ds2) Bacteria
## 119 Fecal>CloacalSwab 0.43365907 DESeq2 man. geoMeans (ds2) Bacteria
## 120 CloacalSwab>Fecal 0.95629167 DESeq2 man. geoMeans (ds2) Bacteria
## 121 Fecal>CloacalSwab 0.42870231 DESeq2 man. geoMeans (ds2) Bacteria
## 122 Fecal>CloacalSwab 0.44620357 DESeq2 man. geoMeans (ds2) Bacteria
## 123 Fecal>CloacalSwab 0.96390562 DESeq2 man. geoMeans (ds2) Bacteria
## 124 Fecal>CloacalSwab 0.54121352 DESeq2 man. geoMeans (ds2) Bacteria
## 125 Fecal>CloacalSwab 0.73586574 DESeq2 man. geoMeans (ds2) Bacteria
## 126 Fecal>CloacalSwab 0.50208662 DESeq2 man. geoMeans (ds2) Bacteria
## 127 Fecal>CloacalSwab 0.55194855 DESeq2 man. geoMeans (ds2) Bacteria
## 128 CloacalSwab>Fecal 0.62105921 DESeq2 man. geoMeans (ds2) Bacteria
## 129 Fecal>CloacalSwab 0.27066597 DESeq2 man. geoMeans (ds2) Bacteria
## 130 Fecal>CloacalSwab 0.70594620 DESeq2 man. geoMeans (ds2) Bacteria
## 131 Fecal>CloacalSwab 0.55194855 DESeq2 man. geoMeans (ds2) Bacteria
## 132 Fecal>CloacalSwab 0.36859448 DESeq2 man. geoMeans (ds2) Bacteria
## 133 CloacalSwab>Fecal 0.93659949 DESeq2 man. geoMeans (ds2)     <NA>
##                        Phylum               Class
## 1              Proteobacteria Gammaproteobacteria
## 2              Proteobacteria Alphaproteobacteria
## 3              Actinobacteria      Actinobacteria
## 4              Actinobacteria      Actinobacteria
## 5                  Firmicutes             Bacilli
## 6              Proteobacteria Gammaproteobacteria
## 7              Actinobacteria      Actinobacteria
## 8               Acidobacteria  Acidobacteria_Gp16
## 9              Actinobacteria      Actinobacteria
## 10             Proteobacteria Alphaproteobacteria
## 11             Actinobacteria      Actinobacteria
## 12             Actinobacteria      Actinobacteria
## 13  Cyanobacteria/Chloroplast         Chloroplast
## 14             Actinobacteria      Actinobacteria
## 15             Proteobacteria Gammaproteobacteria
## 16             Actinobacteria      Actinobacteria
## 17             Actinobacteria      Actinobacteria
## 18             Actinobacteria      Actinobacteria
## 19                Chloroflexi      Thermomicrobia
## 20             Actinobacteria      Actinobacteria
## 21                 Firmicutes    Erysipelotrichia
## 22                Chloroflexi        Chloroflexia
## 23             Proteobacteria Gammaproteobacteria
## 24             Actinobacteria      Actinobacteria
## 25             Actinobacteria      Actinobacteria
## 26             Actinobacteria      Actinobacteria
## 27                 Firmicutes             Bacilli
## 28             Actinobacteria      Actinobacteria
## 29             Actinobacteria      Actinobacteria
## 30             Actinobacteria      Actinobacteria
## 31             Actinobacteria      Actinobacteria
## 32             Actinobacteria      Actinobacteria
## 33             Actinobacteria      Actinobacteria
## 34             Actinobacteria      Actinobacteria
## 35             Actinobacteria      Actinobacteria
## 36                 Firmicutes    Erysipelotrichia
## 37             Proteobacteria Alphaproteobacteria
## 38             Proteobacteria Gammaproteobacteria
## 39             Actinobacteria      Actinobacteria
## 40                 Firmicutes          Clostridia
## 41             Actinobacteria      Actinobacteria
## 42             Actinobacteria      Actinobacteria
## 43             Actinobacteria      Actinobacteria
## 44             Proteobacteria Alphaproteobacteria
## 45                 Firmicutes             Bacilli
## 46             Proteobacteria Alphaproteobacteria
## 47             Actinobacteria      Actinobacteria
## 48             Actinobacteria      Actinobacteria
## 49             Proteobacteria Alphaproteobacteria
## 50             Proteobacteria Gammaproteobacteria
## 51                 Firmicutes          Clostridia
## 52                 Firmicutes          Clostridia
## 53                 Firmicutes          Clostridia
## 54             Actinobacteria      Actinobacteria
## 55                Chloroflexi      Thermomicrobia
## 56             Actinobacteria      Actinobacteria
## 57             Actinobacteria      Actinobacteria
## 58                 Firmicutes          Clostridia
## 59                 Firmicutes          Clostridia
## 60                 Firmicutes          Clostridia
## 61             Actinobacteria      Actinobacteria
## 62  Cyanobacteria/Chloroplast         Chloroplast
## 63             Actinobacteria      Actinobacteria
## 64                 Firmicutes             Bacilli
## 65             Actinobacteria      Actinobacteria
## 66             Proteobacteria Alphaproteobacteria
## 67             Proteobacteria Alphaproteobacteria
## 68             Actinobacteria      Actinobacteria
## 69             Actinobacteria      Actinobacteria
## 70             Actinobacteria      Actinobacteria
## 71             Proteobacteria Alphaproteobacteria
## 72                 Firmicutes    Erysipelotrichia
## 73             Actinobacteria      Actinobacteria
## 74              Bacteroidetes         Bacteroidia
## 75             Proteobacteria Gammaproteobacteria
## 76             Actinobacteria      Actinobacteria
## 77             Actinobacteria      Actinobacteria
## 78             Actinobacteria      Actinobacteria
## 79             Actinobacteria      Actinobacteria
## 80             Actinobacteria      Actinobacteria
## 81             Proteobacteria  Betaproteobacteria
## 82             Proteobacteria Gammaproteobacteria
## 83                 Firmicutes          Clostridia
## 84             Proteobacteria Gammaproteobacteria
## 85             Proteobacteria Alphaproteobacteria
## 86             Actinobacteria      Actinobacteria
## 87             Actinobacteria      Actinobacteria
## 88             Actinobacteria      Actinobacteria
## 89             Proteobacteria Alphaproteobacteria
## 90             Proteobacteria Gammaproteobacteria
## 91             Actinobacteria      Actinobacteria
## 92                 Firmicutes          Clostridia
## 93             Proteobacteria Alphaproteobacteria
## 94             Actinobacteria      Actinobacteria
## 95             Proteobacteria Alphaproteobacteria
## 96             Proteobacteria Gammaproteobacteria
## 97             Actinobacteria      Actinobacteria
## 98             Proteobacteria Alphaproteobacteria
## 99             Proteobacteria Alphaproteobacteria
## 100            Actinobacteria      Actinobacteria
## 101            Actinobacteria      Actinobacteria
## 102            Actinobacteria      Actinobacteria
## 103                Firmicutes             Bacilli
## 104 Cyanobacteria/Chloroplast         Chloroplast
## 105            Proteobacteria Alphaproteobacteria
## 106               Chloroflexi                <NA>
## 107            Actinobacteria      Actinobacteria
## 108            Actinobacteria      Actinobacteria
## 109            Actinobacteria      Actinobacteria
## 110            Actinobacteria      Actinobacteria
## 111            Actinobacteria      Actinobacteria
## 112            Actinobacteria      Actinobacteria
## 113            Actinobacteria      Actinobacteria
## 114            Proteobacteria Gammaproteobacteria
## 115            Actinobacteria      Actinobacteria
## 116            Actinobacteria      Actinobacteria
## 117            Proteobacteria Gammaproteobacteria
## 118           Verrucomicrobia      Spartobacteria
## 119            Actinobacteria      Actinobacteria
## 120                Firmicutes          Clostridia
## 121             Bacteroidetes         Bacteroidia
## 122            Proteobacteria Alphaproteobacteria
## 123           Verrucomicrobia      Spartobacteria
## 124            Proteobacteria Alphaproteobacteria
## 125            Proteobacteria Alphaproteobacteria
## 126            Proteobacteria Gammaproteobacteria
## 127            Actinobacteria      Actinobacteria
## 128 Cyanobacteria/Chloroplast         Chloroplast
## 129                Firmicutes    Erysipelotrichia
## 130                Firmicutes          Clostridia
## 131            Proteobacteria Alphaproteobacteria
## 132                Firmicutes          Clostridia
## 133                      <NA>                <NA>
##                                  Order               Family
## 1                    Oceanospirillales       Halomonadaceae
## 2                          Rhizobiales  Methylobacteriaceae
## 3                  Solirubrobacterales Solirubrobacteraceae
## 4                      Actinomycetales   Pseudonocardiaceae
## 5                      Lactobacillales    Carnobacteriaceae
## 6                    Enterobacteriales   Enterobacteriaceae
## 7                  Solirubrobacterales                 <NA>
## 8                                 Gp16                 <NA>
## 9                  Solirubrobacterales Solirubrobacteraceae
## 10                         Rhizobiales    Xanthobacteraceae
## 11                 Solirubrobacterales Solirubrobacteraceae
## 12                     Actinomycetales      Nocardioidaceae
## 13                         Chloroplast         Streptophyta
## 14                     Actinomycetales    Microbacteriaceae
## 15                   Enterobacteriales   Enterobacteriaceae
## 16                     Rubrobacterales     Rubrobacteraceae
## 17                     Actinomycetales     Mycobacteriaceae
## 18                     Actinomycetales    Microbacteriaceae
## 19                   Sphaerobacterales   Sphaerobacteraceae
## 20                 Solirubrobacterales Solirubrobacteraceae
## 21                  Erysipelotrichales  Erysipelotrichaceae
## 22                       Kallotenuales       Kallotenuaceae
## 23                   Enterobacteriales   Enterobacteriaceae
## 24                     Actinomycetales     Mycobacteriaceae
## 25                     Actinomycetales      Nocardioidaceae
## 26                     Actinomycetales    Microbacteriaceae
## 27                          Bacillales        Bacillaceae_1
## 28                     Actinomycetales    Microbacteriaceae
## 29                     Actinomycetales    Microbacteriaceae
## 30                     Actinomycetales   Intrasporangiaceae
## 31                     Actinomycetales      Nocardioidaceae
## 32                     Actinomycetales    Microbacteriaceae
## 33                     Rubrobacterales     Rubrobacteraceae
## 34                     Rubrobacterales     Rubrobacteraceae
## 35                     Actinomycetales     Mycobacteriaceae
## 36                  Erysipelotrichales  Erysipelotrichaceae
## 37                         Rhizobiales  Methylobacteriaceae
## 38                     Pseudomonadales     Pseudomonadaceae
## 39                     Actinomycetales      Nocardioidaceae
## 40                       Clostridiales      Lachnospiraceae
## 41                     Actinomycetales      Nocardioidaceae
## 42                 Solirubrobacterales Solirubrobacteraceae
## 43                     Actinomycetales Propionibacteriaceae
## 44                         Rhizobiales  Methylobacteriaceae
## 45                     Lactobacillales      Enterococcaceae
## 46                         Rhizobiales    Bradyrhizobiaceae
## 47                     Actinomycetales      Nocardioidaceae
## 48                     Actinomycetales      Nocardioidaceae
## 49                         Rhizobiales  Methylobacteriaceae
## 50                   Enterobacteriales   Enterobacteriaceae
## 51                       Clostridiales      Ruminococcaceae
## 52                       Clostridiales       Eubacteriaceae
## 53                       Clostridiales      Lachnospiraceae
## 54                          Gaiellales          Gaiellaceae
## 55                   Sphaerobacterales   Sphaerobacteraceae
## 56                     Actinomycetales   Pseudonocardiaceae
## 57                     Actinomycetales   Pseudonocardiaceae
## 58                       Clostridiales      Ruminococcaceae
## 59                       Clostridiales      Lachnospiraceae
## 60                       Clostridiales      Lachnospiraceae
## 61                     Actinomycetales Propionibacteriaceae
## 62                         Chloroplast         Streptophyta
## 63                     Actinomycetales                 <NA>
## 64                     Lactobacillales    Carnobacteriaceae
## 65                 Solirubrobacterales    Patulibacteraceae
## 66  Alphaproteobacteria_incertae_sedis         Geminicoccus
## 67                         Rhizobiales         Rhodobiaceae
## 68                     Actinomycetales    Streptomycetaceae
## 69                                <NA>                 <NA>
## 70                     Actinomycetales Propionibacteriaceae
## 71                         Rhizobiales  Methylobacteriaceae
## 72                  Erysipelotrichales  Erysipelotrichaceae
## 73                 Solirubrobacterales                 <NA>
## 74                       Bacteroidales       Bacteroidaceae
## 75                     Pseudomonadales     Pseudomonadaceae
## 76                     Actinomycetales   Pseudonocardiaceae
## 77                     Actinomycetales     Mycobacteriaceae
## 78                     Actinomycetales    Cellulomonadaceae
## 79                     Actinomycetales   Pseudonocardiaceae
## 80                 Solirubrobacterales    Conexibacteraceae
## 81                     Burkholderiales       Alcaligenaceae
## 82                     Pseudomonadales     Pseudomonadaceae
## 83                       Clostridiales      Ruminococcaceae
## 84                     Pseudomonadales        Moraxellaceae
## 85                         Rhizobiales  Methylobacteriaceae
## 86                     Actinomycetales                 <NA>
## 87                     Actinomycetales   Pseudonocardiaceae
## 88                     Actinomycetales    Microbacteriaceae
## 89                         Rhizobiales  Methylobacteriaceae
## 90                   Enterobacteriales   Enterobacteriaceae
## 91                     Actinomycetales      Kineosporiaceae
## 92                       Clostridiales      Ruminococcaceae
## 93  Alphaproteobacteria_incertae_sedis         Geminicoccus
## 94                     Actinomycetales       Micrococcaceae
## 95                    Rhodospirillales           Reyranella
## 96                     Pseudomonadales        Moraxellaceae
## 97                    Coriobacteriales    Coriobacteriaceae
## 98                         Rhizobiales    Hyphomicrobiaceae
## 99                         Rhizobiales  Methylobacteriaceae
## 100                Solirubrobacterales Solirubrobacteraceae
## 101                    Actinomycetales    Sanguibacteraceae
## 102                    Actinomycetales                 <NA>
## 103                         Bacillales    Staphylococcaceae
## 104                        Chloroplast          Chlorophyta
## 105                   Sphingomonadales    Sphingomonadaceae
## 106                               <NA>                 <NA>
## 107                    Actinomycetales     Mycobacteriaceae
## 108                    Actinomycetales         Nocardiaceae
## 109                    Actinomycetales   Pseudonocardiaceae
## 110                    Actinomycetales   Pseudonocardiaceae
## 111                   Acidimicrobiales    Acidimicrobiaceae
## 112                    Actinomycetales Propionibacteriaceae
## 113                    Actinomycetales Propionibacteriaceae
## 114                    Pseudomonadales     Pseudomonadaceae
## 115                   Acidimicrobiales    Acidimicrobiaceae
## 116                    Actinomycetales   Intrasporangiaceae
## 117                    Pseudomonadales     Pseudomonadaceae
## 118                     Terrimicrobium                 <NA>
## 119                         Gaiellales          Gaiellaceae
## 120                      Clostridiales      Ruminococcaceae
## 121                      Bacteroidales       Bacteroidaceae
## 122 Alphaproteobacteria_incertae_sedis         Geminicoccus
## 123                     Terrimicrobium                 <NA>
## 124                        Rhizobiales    Hyphomicrobiaceae
## 125 Alphaproteobacteria_incertae_sedis         Geminicoccus
## 126                  Enterobacteriales   Enterobacteriaceae
## 127                Solirubrobacterales                 <NA>
## 128                        Chloroplast         Streptophyta
## 129                 Erysipelotrichales  Erysipelotrichaceae
## 130                      Clostridiales      Lachnospiraceae
## 131 Alphaproteobacteria_incertae_sedis         Geminicoccus
## 132                      Clostridiales      Lachnospiraceae
## 133                               <NA>                 <NA>
##                 Genus        Species
## 1          Salinicola         socius
## 2    Methylobacterium           <NA>
## 3     Solirubrobacter           <NA>
## 4   Actinomycetospora           <NA>
## 5      Carnobacterium           <NA>
## 6        Buttiauxella           <NA>
## 7                <NA>           <NA>
## 8                <NA>           <NA>
## 9     Solirubrobacter           <NA>
## 10               <NA>           <NA>
## 11    Solirubrobacter           <NA>
## 12       Nocardioides           <NA>
## 13               <NA>           <NA>
## 14         Agrococcus           <NA>
## 15               <NA>           <NA>
## 16        Rubrobacter           <NA>
## 17      Mycobacterium           <NA>
## 18     Curtobacterium           <NA>
## 19               <NA>           <NA>
## 20    Solirubrobacter           <NA>
## 21  Clostridium_XVIII           <NA>
## 22         Kallotenue           <NA>
## 23       Enterobacter           <NA>
## 24      Mycobacterium         JC2972
## 25       Nocardioides           <NA>
## 26     Microbacterium           <NA>
## 27           Bacillus           <NA>
## 28     Curtobacterium           <NA>
## 29     Microbacterium           <NA>
## 30               <NA>           <NA>
## 31       Nocardioides           <NA>
## 32  Pseudoclavibacter       helvolus
## 33        Rubrobacter           <NA>
## 34        Rubrobacter           <NA>
## 35      Mycobacterium           <NA>
## 36  Clostridium_XVIII           <NA>
## 37               <NA>           <NA>
## 38        Pseudomonas           <NA>
## 39       Nocardioides           <NA>
## 40               <NA>           <NA>
## 41       Nocardioides    ginsengagri
## 42    Solirubrobacter           <NA>
## 43       Microlunatus           <NA>
## 44               <NA>           <NA>
## 45       Enterococcus           <NA>
## 46     Bradyrhizobium           <NA>
## 47       Nocardioides           <NA>
## 48       Nocardioides           <NA>
## 49   Methylobacterium           <NA>
## 50            Pantoea           <NA>
## 51     Intestinimonas           <NA>
## 52       Anaerofustis           <NA>
## 53               <NA>           <NA>
## 54            Gaiella           <NA>
## 55      Sphaerobacter           <NA>
## 56  Actinomycetospora           <NA>
## 57     Pseudonocardia           <NA>
## 58               <NA>           <NA>
## 59   Clostridium_XlVa           <NA>
## 60               <NA>           <NA>
## 61       Microlunatus           <NA>
## 62               <NA>           <NA>
## 63               <NA>           <NA>
## 64      Catellicoccus           <NA>
## 65       Patulibacter   minatonensis
## 66               <NA>           <NA>
## 67               <NA>           <NA>
## 68       Streptomyces           <NA>
## 69               <NA>           <NA>
## 70     Friedmanniella           <NA>
## 71         Microvirga     zambiensis
## 72  Clostridium_XVIII           <NA>
## 73               <NA>           <NA>
## 74        Bacteroides           <NA>
## 75        Pseudomonas           <NA>
## 76     Pseudonocardia           <NA>
## 77      Mycobacterium           <NA>
## 78       Cellulomonas           <NA>
## 79     Pseudonocardia           <NA>
## 80       Conexibacter           <NA>
## 81      Achromobacter           <NA>
## 82        Pseudomonas           <NA>
## 83        Anaerofilum           <NA>
## 84      Acinetobacter           <NA>
## 85         Microvirga           <NA>
## 86               <NA>           <NA>
## 87     Pseudonocardia    endophytica
## 88     Microbacterium           <NA>
## 89         Microvirga           <NA>
## 90            Pantoea           <NA>
## 91  Pseudokineococcus           <NA>
## 92     Clostridium_IV           <NA>
## 93               <NA>           <NA>
## 94       Arthrobacter           <NA>
## 95               <NA>           <NA>
## 96      Acinetobacter           <NA>
## 97   Denitrobacterium           <NA>
## 98        Rhodoplanes           <NA>
## 99         Microvirga    lotononidis
## 100   Solirubrobacter           <NA>
## 101      Sanguibacter           <NA>
## 102              <NA>           <NA>
## 103    Staphylococcus           <NA>
## 104              <NA>           <NA>
## 105      Sphingopyxis           <NA>
## 106              <NA>           <NA>
## 107     Mycobacterium           <NA>
## 108       Rhodococcus           <NA>
## 109 Actinomycetospora chiangmaiensis
## 110 Actinomycetospora           <NA>
## 111     Ilumatobacter           <NA>
## 112              <NA>           <NA>
## 113    Friedmanniella           <NA>
## 114       Pseudomonas           <NA>
## 115     Ilumatobacter           <NA>
## 116        Janibacter           <NA>
## 117       Pseudomonas           <NA>
## 118              <NA>           <NA>
## 119           Gaiella           <NA>
## 120    Intestinimonas           <NA>
## 121       Bacteroides           <NA>
## 122              <NA>           <NA>
## 123              <NA>           <NA>
## 124     Pedomicrobium           <NA>
## 125              <NA>           <NA>
## 126           Pantoea           <NA>
## 127              <NA>           <NA>
## 128              <NA>           <NA>
## 129 Clostridium_XVIII           <NA>
## 130  Clostridium_XlVa           <NA>
## 131              <NA>           <NA>
## 132              <NA>           <NA>
## 133              <NA>           <NA>
res.ds2[res.ds2$pval.adj < 0.05,"Feature"]
## [1] NA      NA      "ASV12" NA      "ASV20" NA      NA      NA      "ASV8"
## Three ASVs sig: ASV20, ASV12 and ASV8

## NOTE: some tests don't give back pval.adj values and I just don't use them...

### We can conclude that ASV20 and ASV8 are probably really differentially abundant between fecals and cloacal samples. Let's plot

featurePlot(TxODA, predictor = "Type", feature = "ASV20") + theme_classic()

featurePlot(TxODA, predictor = "Type", feature = "ASV8") + theme_classic()

## Could do this at genus level and phylum level. In between I generally can't think of how to interpret it biologically. You need to merge_taxa and I would suggest when you do that 

## Let's do genus level
## I just use the same tests that worked on the ASV level data for the higher taxa levels. There is not enough information when you merge at higher taxonmic scales to evalutae the methods
TxO_G <- tax_glom(TxO, taxrank = "Genus")


TxO_G
## phyloseq-class experiment-level object
## otu_table()   OTU Table:         [ 155 taxa and 12 samples ]
## sample_data() Sample Data:       [ 12 samples by 21 sample variables ]
## tax_table()   Taxonomy Table:    [ 155 taxa by 7 taxonomic ranks ]
## refseq()      DNAStringSet:      [ 155 reference sequences ]
## Testing 199 genera

res.liaG <- DA.lia(TxO_G, predictor = "Type")
res.liaG
##     Feature        logFC       AveExpr           t         pval
## 1     ASV10 -1.497860867  0.5032085171 -1.70254422 1.133706e-01
## 2    ASV100 -1.791852439  1.1394818842 -5.26658693 1.736398e-04
## 3   ASV1003 -0.245721916 -0.1228609582 -1.25644812 2.319270e-01
## 4    ASV101 -0.653397888  0.0809770274 -1.57914060 1.392641e-01
## 5   ASV1027  0.379378705  0.1896893523  1.03411076 3.206770e-01
## 6    ASV103  1.953201765  1.9924328463  3.62812975 3.251163e-03
## 7   ASV1046  0.094441978  0.0280811122  0.31347005 7.590927e-01
## 8   ASV1067 -0.479336507 -0.0060536631 -1.67486793 1.187778e-01
## 9    ASV107 -0.756823436  0.1326898015 -2.40793760 3.229339e-02
## 10    ASV11 -0.218481214  1.1073250019 -0.20288488 8.424900e-01
## 11  ASV1108 -0.342106570 -0.0746686315 -1.60067567 1.344054e-01
## 12  ASV1122 -0.454773782 -0.0183350252 -1.68079470 1.176012e-01
## 13   ASV113 -0.899621845  0.2040890059 -2.43208398 3.088179e-02
## 14  ASV1136  0.168109523  0.2480169328  0.53050648 6.050577e-01
## 15  ASV1179  0.195118023  0.1939436652  0.63638391 5.360056e-01
## 16  ASV1184 -0.189099660 -0.1511720862 -0.95328051 3.585189e-01
## 17   ASV121 -0.272046078  0.6053767006 -0.47579977 6.424245e-01
## 18  ASV1211 -0.336683339 -0.0773802469 -1.58950612 1.369068e-01
## 19  ASV1214 -0.342106570 -0.0746686315 -1.60067567 1.344054e-01
## 20  ASV1241 -0.245721916 -0.1228609582 -1.25644812 2.319270e-01
## 21  ASV1262  0.152715122  0.0763575610  0.81044921 4.328412e-01
## 22   ASV129 -1.167366387  0.3379612769 -2.01629914 6.577952e-02
## 23  ASV1318  0.390820762  0.1954103808  0.97607186 3.475407e-01
## 24   ASV134  0.600708100  0.3003540502  0.93083714 3.695668e-01
## 25  ASV1382  0.115524530  0.0577622650  0.51013770 6.188427e-01
## 26   ASV139 -1.030914209  0.3553246675 -2.11830835 5.480872e-02
## 27  ASV1397 -0.245721916 -0.1228609582 -1.25644812 2.319270e-01
## 28  ASV1400 -0.406826770 -0.0423085312 -1.67473056 1.188052e-01
## 29  ASV1427 -0.187487526 -0.0937437629 -0.77706654 4.515749e-01
## 30  ASV1443 -0.245721916 -0.1228609582 -1.25644812 2.319270e-01
## 31  ASV1470 -0.098851296 -0.0685655248 -0.37177625 7.162852e-01
## 32  ASV1473 -0.182988729 -0.0914943647 -1.17462603 2.620360e-01
## 33  ASV1485 -0.245721916 -0.1228609582 -1.25644812 2.319270e-01
## 34    ASV15 -0.615543612  0.8318431218 -0.81481409 4.304295e-01
## 35   ASV155 -0.907244155  0.2079001611 -1.68854314 1.160783e-01
## 36  ASV1553 -0.183897906 -0.0919489529 -0.81892314 4.281672e-01
## 37   ASV170 -0.352753146  0.6255976632 -0.67105611 5.143939e-01
## 38   ASV175  0.389672973  0.1756966099  0.62333279 5.442720e-01
## 39   ASV176 -1.012706731  0.2606314490 -2.11738320 5.490005e-02
## 40   ASV177 -0.131120698  1.0349337602 -0.20226952 8.429607e-01
## 41  ASV1787 -0.223724722 -0.1338595553 -1.13822463 2.763722e-01
## 42  ASV1814 -0.303012056 -0.1515060279 -1.46166489 1.685129e-01
## 43  ASV1826 -0.273077005 -0.1365385026 -1.28909248 2.207105e-01
## 44  ASV1828 -0.454773782 -0.0183350252 -1.68079470 1.176012e-01
## 45   ASV183 -0.149480027  1.7789888662 -0.21056077 8.366234e-01
## 46   ASV185 -0.456955388 -0.0172442223 -1.68046010 1.176673e-01
## 47    ASV19  0.327216177  1.9763112709  0.30149227 7.679960e-01
## 48   ASV190 -0.749069574  0.1288128707 -2.49686921 2.738194e-02
## 49  ASV1922 -0.119910008 -0.0599550039 -0.78757017 4.456255e-01
## 50   ASV193  2.042283513  1.2323752282  6.82382038 1.491243e-05
## 51     ASV2 -1.168831040  0.5168380018 -1.17431059 2.621577e-01
## 52   ASV204 -0.230298784  0.3163767201 -0.47589410 6.423591e-01
## 53   ASV207 -0.245721916 -0.1228609582 -1.25644812 2.319270e-01
## 54   ASV214 -1.548021105  0.5282886363 -3.69530668 2.867265e-03
## 55   ASV215  1.889548930  1.0411591187  7.54946793 5.308128e-06
## 56   ASV216 -0.495077422  0.0018167945 -1.55788238 1.442084e-01
## 57  ASV2179 -0.158461652 -0.0792308258 -0.70031038 4.965616e-01
## 58   ASV221 -0.137530445  0.4738357071 -0.25299600 8.043841e-01
## 59   ASV223  0.640878384  0.2958760844  2.30443517 3.907631e-02
## 60   ASV226 -0.760204026  0.1343800968 -1.52042028 1.532894e-01
## 61    ASV23  0.198899672  1.2821213233  0.18059853 8.595777e-01
## 62   ASV235 -0.746067399  0.1273117830 -1.92698478 7.701798e-02
## 63   ASV236 -0.628942549  0.0687493579 -1.90699541 7.976302e-02
## 64   ASV237 -0.245721916 -0.1228609582 -1.25644812 2.319270e-01
## 65   ASV248  0.444217799  0.2221088995  1.42803210 1.777877e-01
## 66   ASV253  0.914877279  0.7171097528  2.40819275 3.227815e-02
## 67   ASV256  0.019695794  0.2217570805  0.04548985 9.644355e-01
## 68   ASV258 -0.341430858 -0.0750064873 -1.59933294 1.347040e-01
## 69    ASV26 -0.882767916  2.3642085665 -1.84760021 8.845337e-02
## 70   ASV265 -0.721940194  0.1152481805 -1.86790390 8.539047e-02
## 71   ASV267  0.960848500  0.7856027313  1.71471355 1.110627e-01
## 72   ASV270 -0.938362342  0.2234592545 -1.67899947 1.179565e-01
## 73   ASV273 -0.862449754  0.1855029604 -1.73610889 1.071059e-01
## 74   ASV274 -0.245721916 -0.1228609582 -1.25644812 2.319270e-01
## 75    ASV29 -0.013447636  0.7234288721 -0.01600085 9.874863e-01
## 76   ASV291 -0.786352817  0.1474544920 -1.99943867 6.777787e-02
## 77   ASV293 -0.226582040 -0.1324308965 -1.15416697 2.700211e-01
## 78   ASV296 -0.550224686  0.0293904267 -1.64101440 1.256995e-01
## 79    ASV30 -0.776840056  1.3341914068 -1.05444168 3.116358e-01
## 80   ASV303  0.380282447  0.1462933816  1.12864447 2.802435e-01
## 81   ASV306 -0.037389965  0.1452671892 -0.12562792 9.020244e-01
## 82    ASV31 -1.815486676  0.7897521651 -2.17367324 4.959497e-02
## 83   ASV311 -0.470113727 -0.0106650531 -1.56405566 1.427573e-01
## 84   ASV312 -0.553340042  0.0309481045 -2.02241562 6.506814e-02
## 85   ASV318  0.243103789  0.1215518947  0.69695586 4.985875e-01
## 86   ASV332  0.179684732  0.7243443797  0.30563936 7.649094e-01
## 87   ASV334 -0.494145980  0.0013510737 -1.66939636 1.198733e-01
## 88   ASV337  0.407027207  0.2035136035  0.79505489 4.414168e-01
## 89   ASV338 -0.525516721  0.0170364441 -1.54751982 1.466729e-01
## 90   ASV342 -0.245721916 -0.1228609582 -1.25644812 2.319270e-01
## 91   ASV348 -0.574218104  0.1014270424 -1.31661676 2.115964e-01
## 92   ASV349  0.399747088  0.1998735440  1.11890340 2.842221e-01
## 93   ASV356 -0.316867751 -0.0872880411 -1.46456435 1.677328e-01
## 94   ASV359 -0.497788193  0.0031721801 -1.55770542 1.442502e-01
## 95   ASV375  0.120115498  0.9528485497  0.25522307 8.027018e-01
## 96   ASV376 -0.179621493  0.0495883175 -0.66003276 5.212094e-01
## 97   ASV378 -0.226582040 -0.1324308965 -1.15416697 2.700211e-01
## 98   ASV381 -0.301699058  0.1088215841 -1.00159122 3.355360e-01
## 99   ASV387 -0.245721916 -0.1228609582 -1.25644812 2.319270e-01
## 100  ASV388 -0.245721916 -0.1228609582 -1.25644812 2.319270e-01
## 101  ASV416  0.237395425  0.1186977125  0.61880002 5.471596e-01
## 102   ASV43 -0.332100429  1.8570550387 -0.54383977 5.961185e-01
## 103   ASV44  0.108549090  1.4863015379  0.17116720 8.668319e-01
## 104  ASV440 -0.552111831 -0.0269561402 -1.81420219 9.370823e-02
## 105  ASV445 -0.491964374  0.0002602708 -1.67027530 1.196968e-01
## 106  ASV451  1.676186719  1.0500025433  4.77666681 4.029273e-04
## 107  ASV467 -0.245721916 -0.1228609582 -1.25644812 2.319270e-01
## 108  ASV472  0.321693253  0.1608466267  1.01696835 3.284486e-01
## 109  ASV473 -0.226582040 -0.1324308965 -1.15416697 2.700211e-01
## 110  ASV474 -0.245721916 -0.1228609582 -1.25644812 2.319270e-01
## 111  ASV475 -0.221013951 -0.1352149408 -1.12296227 2.825591e-01
## 112  ASV483 -0.241725340  0.3084818359 -0.47205386 6.450223e-01
## 113  ASV506 -0.409008376 -0.0412177283 -1.67569224 1.186136e-01
## 114  ASV517 -0.580215026  0.0443855965 -1.98702309 6.928506e-02
## 115  ASV520 -0.475006104 -0.0082188646 -1.58837188 1.371630e-01
## 116   ASV53 -2.158895989  0.8337260779 -2.89040906 1.308004e-02
## 117  ASV531 -0.301884141  0.0609671132 -1.24021642 2.376711e-01
## 118  ASV538 -0.548043080  0.0282996238 -1.64226147 1.254384e-01
## 119   ASV54  0.869559098  0.8152888846  1.03254157 3.213827e-01
## 120  ASV558 -0.456955388 -0.0172442223 -1.68046010 1.176673e-01
## 121  ASV562  0.439080054  0.2195400271  1.21301026 2.475511e-01
## 122  ASV566 -0.683071847  0.0958140071 -2.09412069 5.724388e-02
## 123  ASV572 -0.485160325 -0.0031417538 -2.01139332 6.635528e-02
## 124  ASV585  0.509339241  0.2546696205  1.10863003 2.884644e-01
## 125  ASV586 -0.030386926 -0.0151934631 -0.11381975 9.111884e-01
## 126  ASV588 -0.437039177 -0.0545574169 -1.69628154 1.145748e-01
## 127  ASV593 -0.006813863  0.1837942870 -0.02572862 9.798800e-01
## 128    ASV6 -2.664992519  1.5178175340 -3.42567285 4.756006e-03
## 129   ASV60 -0.924410093  0.2164831302 -1.44947211 1.718271e-01
## 130  ASV605  0.783533594  0.7192005109  1.06063723 3.089185e-01
## 131   ASV62 -1.965051964  0.7760935871 -3.40169302 4.975893e-03
## 132  ASV641 -0.245721916 -0.1228609582 -1.25644812 2.319270e-01
## 133  ASV645 -0.460885078  0.1903334284 -1.15293590 2.705075e-01
## 134  ASV647 -0.245721916 -0.1228609582 -1.25644812 2.319270e-01
## 135  ASV652  1.027586133  0.5137930663  2.83318738 1.457213e-02
## 136  ASV665 -0.285484314 -0.1029797595 -1.30449250 2.155728e-01
## 137   ASV68  0.849823366  1.6663464942  1.59854441 1.348796e-01
## 138   ASV69  0.559688018  0.8747211983  1.01839068 3.277986e-01
## 139  ASV716 -0.138412599 -0.0883461759 -0.86973339 4.008388e-01
## 140  ASV728  1.086213726  0.7550160468  2.90609890 1.269804e-02
## 141  ASV776 -0.522351300  0.0154537338 -1.65625765 1.225403e-01
## 142  ASV784  0.034452168  0.0172260842  0.21331744 8.345190e-01
## 143  ASV785 -0.336683339 -0.0773802469 -1.58950612 1.369068e-01
## 144    ASV8 -3.777785435  2.2885419296 -7.24424184 8.130275e-06
## 145  ASV809 -0.065358292 -0.0326791459 -0.23334325 8.192724e-01
## 146   ASV81  0.400730829  0.6963992804  0.55866110 5.862617e-01
## 147   ASV82 -1.617191100  0.5628736335 -2.76111643 1.669245e-02
## 148  ASV850  0.238304601  0.1191523007  1.23580713 2.392508e-01
## 149   ASV87  0.300784793  1.1608074047  0.36979140 7.177271e-01
## 150    ASV9 -0.103933099  0.7594946773 -0.08889676 9.305724e-01
## 151  ASV906  0.111139052  0.0555695262  0.35807593 7.262605e-01
## 152   ASV91  1.133460036  1.8158082017  1.50357766 1.575288e-01
## 153   ASV95 -0.788025039  0.1482906032 -1.50677547 1.567163e-01
## 154  ASV999 -0.180882822 -0.0904414110 -0.83694900 4.183349e-01
##         pval.adj          B          ordering            Method  Kingdom
## 1   0.3641727070 -5.2116738 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 2   0.0066851314  1.0293298 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 3   0.4105374648 -5.8034773 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 4   0.3641727070 -5.3875434 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 5   0.4713613195 -6.0471020 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 6   0.0715255890 -1.8651274 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 7   0.8508732289 -6.5386524 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 8   0.3641727070 -5.2518441 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 9   0.2925401085 -4.0759136 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 10  0.8891503738 -6.5687462 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 11  0.3641727070 -5.3574666 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 12  0.3641727070 -5.2432762 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 13  0.2925401085 -4.0340953 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 14  0.7223169051 -6.4430448 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 15  0.6656843327 -6.3793442 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 16  0.5019265231 -6.1258875 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 17  0.7468679745 -6.4716316 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 18  0.3641727070 -5.3730998 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 19  0.3641727070 -5.3574666 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 20  0.4105374648 -5.8034773 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 21  0.5746339932 -6.2513974 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 22  0.3641727070 -4.7302417 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 23  0.4910208050 -6.1042262 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 24  0.5127323435 -6.1467865 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 25  0.7330906101 -6.4540367 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 26  0.3641727070 -4.5647163 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 27  0.4105374648 -5.8034773 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 28  0.3641727070 -5.2520424 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 29  0.5843910393 -6.2781127 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 30  0.4105374648 -5.8034773 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 31  0.8187405040 -6.5176781 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 32  0.4339390419 -5.8975462 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 33  0.4105374648 -5.8034773 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 34  0.5746339932 -6.2478296 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 35  0.3641727070 -5.2320465 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 36  0.5746339932 -6.2444551 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 37  0.6493169424 -6.3561270 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 38  0.6687505828 -6.3877851 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 39  0.3641727070 -4.5662347 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 40  0.8891503738 -6.5688779 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 41  0.4377019993 -5.9377760 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 42  0.3873281729 -5.5467539 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 43  0.4105374648 -5.7645809 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 44  0.3641727070 -5.2432762 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 45  0.8891503738 -6.5670700 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 46  0.3641727070 -5.2437604 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 47  0.8508732289 -6.5425266 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 48  0.2925401085 -3.9212094 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 49  0.5815790013 -6.2698163 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 50  0.0007655049  3.4421663 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 51  0.4339390419 -5.8978992 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 52  0.7468679745 -6.4715849 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 53  0.4105374648 -5.8034773 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 54  0.0715255890 -1.7417685 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 55  0.0006260312  4.4431403 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 56  0.3641727070 -5.4169692 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 57  0.6345659031 -6.3356489 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 58  0.8785471616 -6.5566897 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 59  0.3343195832 -4.2534500 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 60  0.3732220856 -5.4681723 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 61  0.9005099833 -6.5732624 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 62  0.3641727070 -4.8718035 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 63  0.3641727070 -4.9030251 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 64  0.4105374648 -5.8034773 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 65  0.3968015085 -5.5907574 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 66  0.2925401085 -4.0754725 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 67  0.9771254762 -6.5894297 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 68  0.3641727070 -5.3593497 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 69  0.3641727070 -4.9947452 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 70  0.3641727070 -4.9635715 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 71  0.3641727070 -5.1938825 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 72  0.3641727070 -5.2458734 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 73  0.3641727070 -5.1624162 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 74  0.4105374648 -5.8034773 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 75  0.9874862784 -6.5903907 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 76  0.3641727070 -4.7572154 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 77  0.4339390419 -5.9202821 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 78  0.3641727070 -5.3004179 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 79  0.4659409472 -6.0264356 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 80  0.4377019993 -5.9481939 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 81  0.9322936973 -6.5821668 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 82  0.3641727070 -4.4733040 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 83  0.3641727070 -5.4084514 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 84  0.3641727070 -4.7204285 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 85  0.6345659031 -6.3380381 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 86  0.8508732289 -6.5412021 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 87  0.3641727070 -5.2597371 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 88  0.5810100965 -6.2638430 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 89  0.3643166587 -5.4312166 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 90  0.4105374648 -5.8034773 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 91  0.4105374648 -5.7311967 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 92  0.4377019993 -5.9587134 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 93  0.3873281729 -5.5429266 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 94  0.3641727070 -5.4172130 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 95  0.8785471616 -6.5560930 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 96  0.6525711010 -6.3636329 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 97  0.4339390419 -5.9202821 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 98  0.4784494553 -6.0794536 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 99  0.4105374648 -5.8034773 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 100 0.4105374648 -5.8034773 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 101 0.6687505828 -6.3906783 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 102 0.7172050847 -6.4356270 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 103 0.9019737361 -6.5750163 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 104 0.3641727070 -5.0456050 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 105 0.3641727070 -5.2584703 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 106 0.0124101602  0.1962344 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 107 0.4105374648 -5.8034773 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 108 0.4727204739 -6.0642646 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 109 0.4339390419 -5.9202821 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 110 0.4105374648 -5.8034773 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 111 0.4377019993 -5.9543392 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 112 0.7468679745 -6.4734796 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 113 0.3641727070 -5.2506536 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 114 0.3641727070 -4.7770052 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 115 0.3641727070 -5.3746833 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 116 0.1831206294 -3.2184805 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 117 0.4139845220 -5.8225315 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 118 0.3641727070 -5.2986397 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 119 0.4713613195 -6.0486830 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 120 0.3641727070 -5.2437604 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 121 0.4235874942 -5.8540355 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 122 0.3641727070 -4.6043142 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 123 0.3641727070 -4.7381018 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 124 0.4398368769 -5.9697273 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 125 0.9354867514 -6.5836637 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 126 0.3641727070 -5.2207993 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 127 0.9862844312 -6.5901755 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 128 0.0851430528 -2.2376078 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 129 0.3891379208 -5.5627900 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 130 0.4659409472 -6.0200711 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 131 0.0851430528 -2.2817555 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 132 0.4105374648 -5.8034773 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 133 0.4339390419 -5.9216400 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 134 0.4105374648 -5.8034773 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 135 0.1870089854 -3.3220995 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 136 0.4105374648 -5.7459679 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 137 0.3641727070 -5.3604551 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 138 0.4727204739 -6.0628498 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 139 0.5511533387 -6.2014799 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 140 0.1831206294 -3.1900043 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 141 0.3641727070 -5.2786241 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 142 0.8891503738 -6.5664529 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 143 0.3641727070 -5.3730998 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 144 0.0006260312  4.0313488 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 145 0.8885066780 -6.5617313 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 146 0.7109000350 -6.4271756 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 147 0.1977413366 -3.4520236 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 148 0.4139845220 -5.8276743 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 149 0.8187405040 -6.5184496 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 150 0.9490605851 -6.5863392 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 151 0.8223831904 -6.5229210 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 152 0.3732220856 -5.4909165 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 153 0.3732220856 -5.4866116 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 154 0.5701201829 -6.2294726 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
##                  Phylum               Class               Order
## 1        Proteobacteria Gammaproteobacteria   Oceanospirillales
## 2        Proteobacteria Alphaproteobacteria         Rhizobiales
## 3        Actinobacteria      Actinobacteria     Actinomycetales
## 4         Bacteroidetes    Sphingobacteriia  Sphingobacteriales
## 5        Proteobacteria Alphaproteobacteria         Rhizobiales
## 6        Actinobacteria      Actinobacteria Solirubrobacterales
## 7        Actinobacteria      Actinobacteria     Actinomycetales
## 8        Proteobacteria  Betaproteobacteria     Burkholderiales
## 9            Firmicutes             Bacilli     Lactobacillales
## 10       Proteobacteria Gammaproteobacteria   Enterobacteriales
## 11        Bacteroidetes         Bacteroidia       Bacteroidales
## 12         Fusobacteria       Fusobacteriia     Fusobacteriales
## 13        Bacteroidetes      Flavobacteriia    Flavobacteriales
## 14       Actinobacteria      Actinobacteria    Acidimicrobiales
## 15       Actinobacteria      Actinobacteria     Actinomycetales
## 16        Bacteroidetes          Cytophagia        Cytophagales
## 17       Actinobacteria      Actinobacteria     Actinomycetales
## 18        Bacteroidetes      Flavobacteriia    Flavobacteriales
## 19       Proteobacteria Alphaproteobacteria         Rhizobiales
## 20       Actinobacteria      Actinobacteria   Bifidobacteriales
## 21       Proteobacteria Alphaproteobacteria         Rhizobiales
## 22       Proteobacteria  Betaproteobacteria     Burkholderiales
## 23       Actinobacteria      Actinobacteria     Actinomycetales
## 24           Firmicutes       Negativicutes     Selenomonadales
## 25       Actinobacteria      Actinobacteria     Actinomycetales
## 26       Proteobacteria Alphaproteobacteria         Rhizobiales
## 27       Proteobacteria Alphaproteobacteria     Caulobacterales
## 28        Bacteroidetes         Bacteroidia       Bacteroidales
## 29          Nitrospirae          Nitrospira       Nitrospirales
## 30       Actinobacteria      Actinobacteria     Actinomycetales
## 31          Chloroflexi        Chloroflexia       Kallotenuales
## 32       Proteobacteria Deltaproteobacteria        Myxococcales
## 33       Actinobacteria      Actinobacteria     Actinomycetales
## 34       Proteobacteria Gammaproteobacteria   Enterobacteriales
## 35       Proteobacteria  Betaproteobacteria     Burkholderiales
## 36       Proteobacteria Alphaproteobacteria     Rhodobacterales
## 37       Actinobacteria      Actinobacteria     Actinomycetales
## 38       Proteobacteria Deltaproteobacteria  Desulfovibrionales
## 39       Actinobacteria      Actinobacteria     Actinomycetales
## 40           Firmicutes             Bacilli          Bacillales
## 41       Proteobacteria  Betaproteobacteria     Burkholderiales
## 42       Planctomycetes      Planctomycetia    Planctomycetales
## 43       Actinobacteria      Actinobacteria    Acidimicrobiales
## 44     Gemmatimonadetes    Gemmatimonadetes    Gemmatimonadales
## 45       Actinobacteria      Actinobacteria     Actinomycetales
## 46           Firmicutes             Bacilli          Bacillales
## 47           Firmicutes             Bacilli     Lactobacillales
## 48       Actinobacteria      Actinobacteria     Actinomycetales
## 49       Proteobacteria Deltaproteobacteria        Myxococcales
## 50       Actinobacteria      Actinobacteria     Rubrobacterales
## 51       Proteobacteria Gammaproteobacteria       Legionellales
## 52       Actinobacteria      Actinobacteria     Actinomycetales
## 53       Proteobacteria Gammaproteobacteria   Enterobacteriales
## 54       Proteobacteria Alphaproteobacteria    Sphingomonadales
## 55       Actinobacteria      Actinobacteria     Actinomycetales
## 56        Bacteroidetes          Cytophagia        Cytophagales
## 57       Proteobacteria Alphaproteobacteria         Rhizobiales
## 58       Actinobacteria      Actinobacteria     Actinomycetales
## 59       Proteobacteria Alphaproteobacteria         Rhizobiales
## 60           Firmicutes             Bacilli     Lactobacillales
## 61           Firmicutes             Bacilli     Lactobacillales
## 62        Bacteroidetes    Sphingobacteriia  Sphingobacteriales
## 63       Proteobacteria Gammaproteobacteria     Alteromonadales
## 64       Actinobacteria      Actinobacteria     Actinomycetales
## 65           Firmicutes          Clostridia       Clostridiales
## 66       Actinobacteria      Actinobacteria          Gaiellales
## 67          Chloroflexi      Thermomicrobia   Sphaerobacterales
## 68  Deinococcus-Thermus          Deinococci           Thermales
## 69       Actinobacteria      Actinobacteria     Actinomycetales
## 70       Proteobacteria Alphaproteobacteria         Rhizobiales
## 71           Firmicutes          Clostridia       Clostridiales
## 72       Actinobacteria      Actinobacteria     Actinomycetales
## 73       Proteobacteria Gammaproteobacteria     Xanthomonadales
## 74        Bacteroidetes    Sphingobacteriia  Sphingobacteriales
## 75           Firmicutes             Bacilli     Lactobacillales
## 76       Proteobacteria Alphaproteobacteria         Rhizobiales
## 77        Bacteroidetes         Bacteroidia       Bacteroidales
## 78           Firmicutes          Clostridia       Clostridiales
## 79       Actinobacteria      Actinobacteria Solirubrobacterales
## 80       Actinobacteria      Actinobacteria     Actinomycetales
## 81       Actinobacteria      Actinobacteria     Actinomycetales
## 82       Actinobacteria      Actinobacteria     Actinomycetales
## 83           Firmicutes          Clostridia       Clostridiales
## 84           Firmicutes             Bacilli     Lactobacillales
## 85           Firmicutes          Clostridia       Clostridiales
## 86        Bacteroidetes         Bacteroidia       Bacteroidales
## 87           Firmicutes             Bacilli          Bacillales
## 88       Actinobacteria      Actinobacteria     Actinomycetales
## 89       Proteobacteria Alphaproteobacteria     Rhodobacterales
## 90       Proteobacteria Gammaproteobacteria     Xanthomonadales
## 91       Actinobacteria      Actinobacteria     Actinomycetales
## 92       Actinobacteria      Actinobacteria     Actinomycetales
## 93       Actinobacteria      Actinobacteria     Actinomycetales
## 94       Proteobacteria  Betaproteobacteria     Burkholderiales
## 95       Actinobacteria      Actinobacteria Solirubrobacterales
## 96       Proteobacteria  Betaproteobacteria     Burkholderiales
## 97       Proteobacteria Alphaproteobacteria         Rhizobiales
## 98           Firmicutes          Clostridia       Clostridiales
## 99       Proteobacteria  Betaproteobacteria     Burkholderiales
## 100          Firmicutes    Erysipelotrichia  Erysipelotrichales
## 101          Firmicutes             Bacilli          Bacillales
## 102      Actinobacteria      Actinobacteria     Actinomycetales
## 103      Actinobacteria      Actinobacteria     Actinomycetales
## 104      Proteobacteria Alphaproteobacteria     Rhodobacterales
## 105       Bacteroidetes      Flavobacteriia    Flavobacteriales
## 106      Proteobacteria Alphaproteobacteria         Rhizobiales
## 107      Proteobacteria Alphaproteobacteria    Sphingomonadales
## 108      Actinobacteria      Actinobacteria     Actinomycetales
## 109          Firmicutes          Clostridia       Clostridiales
## 110      Actinobacteria      Actinobacteria     Actinomycetales
## 111      Proteobacteria Alphaproteobacteria         Rhizobiales
## 112      Actinobacteria      Actinobacteria     Actinomycetales
## 113      Proteobacteria Alphaproteobacteria    Sphingomonadales
## 114      Actinobacteria      Actinobacteria     Actinomycetales
## 115      Proteobacteria Alphaproteobacteria     Rhodobacterales
## 116      Proteobacteria Gammaproteobacteria     Pseudomonadales
## 117      Actinobacteria      Actinobacteria     Actinomycetales
## 118 Deinococcus-Thermus          Deinococci       Deinococcales
## 119      Actinobacteria      Actinobacteria    Coriobacteriales
## 120          Firmicutes       Negativicutes     Selenomonadales
## 121      Proteobacteria Alphaproteobacteria         Rhizobiales
## 122      Actinobacteria      Actinobacteria     Actinomycetales
## 123      Proteobacteria Gammaproteobacteria     Pseudomonadales
## 124      Actinobacteria      Actinobacteria    Acidimicrobiales
## 125          Firmicutes             Bacilli          Bacillales
## 126          Firmicutes          Clostridia       Clostridiales
## 127      Actinobacteria      Actinobacteria     Actinomycetales
## 128      Actinobacteria      Actinobacteria     Actinomycetales
## 129          Firmicutes          Clostridia       Clostridiales
## 130          Firmicutes          Clostridia       Clostridiales
## 131          Firmicutes             Bacilli          Bacillales
## 132      Proteobacteria Alphaproteobacteria         Rhizobiales
## 133      Proteobacteria Alphaproteobacteria         Rhizobiales
## 134      Proteobacteria Alphaproteobacteria         Rhizobiales
## 135         Chloroflexi      Thermomicrobia   Sphaerobacterales
## 136      Proteobacteria Alphaproteobacteria    Sphingomonadales
## 137      Actinobacteria      Actinobacteria     Actinomycetales
## 138      Actinobacteria      Actinobacteria     Actinomycetales
## 139          Firmicutes          Clostridia       Clostridiales
## 140      Actinobacteria      Actinobacteria    Acidimicrobiales
## 141      Proteobacteria Alphaproteobacteria     Caulobacterales
## 142      Actinobacteria      Actinobacteria     Actinomycetales
## 143      Proteobacteria  Betaproteobacteria     Burkholderiales
## 144      Proteobacteria Gammaproteobacteria     Pseudomonadales
## 145          Firmicutes          Clostridia       Clostridiales
## 146          Firmicutes          Clostridia       Clostridiales
## 147      Proteobacteria Gammaproteobacteria     Xanthomonadales
## 148      Proteobacteria Alphaproteobacteria         Rhizobiales
## 149      Proteobacteria Gammaproteobacteria   Enterobacteriales
## 150          Firmicutes             Bacilli     Lactobacillales
## 151          Firmicutes             Bacilli          Bacillales
## 152          Firmicutes    Erysipelotrichia  Erysipelotrichales
## 153      Proteobacteria Gammaproteobacteria   Oceanospirillales
## 154       Bacteroidetes         Bacteroidia       Bacteroidales
##                                Family                     Genus Species
## 1                      Halomonadaceae                Salinicola    <NA>
## 2                 Methylobacteriaceae          Methylobacterium    <NA>
## 3                      Micrococcaceae                   Kocuria    <NA>
## 4                 Sphingobacteriaceae          Sphingobacterium    <NA>
## 5                  Phyllobacteriaceae             Mesorhizobium    <NA>
## 6                Solirubrobacteraceae           Solirubrobacter    <NA>
## 7                  Micromonosporaceae                    Asanoa    <NA>
## 8                      Comamonadaceae                Acidovorax    <NA>
## 9                   Carnobacteriaceae            Carnobacterium    <NA>
## 10                 Enterobacteriaceae              Buttiauxella    <NA>
## 11                 Porphyromonadaceae           Parabacteroides    <NA>
## 12                   Fusobacteriaceae             Fusobacterium    <NA>
## 13                  Flavobacteriaceae          Chryseobacterium    <NA>
## 14                          Iamiaceae                     Iamia    <NA>
## 15               Propionibacteriaceae         Mariniluteicoccus    <NA>
## 16                      Cytophagaceae               Dyadobacter    <NA>
## 17                  Microbacteriaceae                Agrococcus    <NA>
## 18                  Flavobacteriaceae          Leeuwenhoekiella    <NA>
## 19                  Bradyrhizobiaceae                     Bosea    <NA>
## 20                 Bifidobacteriaceae           Bifidobacterium    <NA>
## 21                  Hyphomicrobiaceae            Hyphomicrobium    <NA>
## 22                     Comamonadaceae                   Delftia    <NA>
## 23                 Micromonosporaceae              Actinoplanes    <NA>
## 24                    Veillonellaceae                 Pelosinus    <NA>
## 25                    Acidothermaceae              Acidothermus    <NA>
## 26                       Rhizobiaceae                 Rhizobium    <NA>
## 27                   Caulobacteraceae               Caulobacter    <NA>
## 28                     Prevotellaceae                Prevotella    <NA>
## 29                     Nitrospiraceae                Nitrospira    <NA>
## 30                     Micrococcaceae                    Rothia    <NA>
## 31                     Kallotenuaceae                Kallotenue    <NA>
## 32                   Labilitrichaceae               Labilithrix    <NA>
## 33                  Microbacteriaceae                 Leifsonia    <NA>
## 34                 Enterobacteriaceae              Enterobacter    <NA>
## 35                   Burkholderiaceae                 Ralstonia    <NA>
## 36                   Rhodobacteraceae               Amaricoccus    <NA>
## 37                  Microbacteriaceae            Curtobacterium    <NA>
## 38                Desulfovibrionaceae             Desulfovibrio    <NA>
## 39               Propionibacteriaceae         Propionibacterium    <NA>
## 40                      Bacillaceae_1                  Bacillus    <NA>
## 41                     Comamonadaceae                 Comamonas    <NA>
## 42                  Planctomycetaceae                   Gemmata    <NA>
## 43                          Iamiaceae              Aquihabitans    <NA>
## 44                  Gemmatimonadaceae              Gemmatimonas    <NA>
## 45                    Nocardioidaceae              Nocardioides    <NA>
## 46       Bacillales_Incertae_Sedis_XI                   Gemella    <NA>
## 47                    Enterococcaceae              Enterococcus    <NA>
## 48                  Microbacteriaceae         Pseudoclavibacter    <NA>
## 49                      Myxococcaceae                Myxococcus    <NA>
## 50                   Rubrobacteraceae               Rubrobacter    <NA>
## 51                       Coxiellaceae           Diplorickettsia    <NA>
## 52                       Nocardiaceae                Williamsia    <NA>
## 53                 Enterobacteriaceae                  Serratia    <NA>
## 54                  Sphingomonadaceae              Sphingomonas    <NA>
## 55               Propionibacteriaceae              Microlunatus    <NA>
## 56                      Cytophagaceae              Hymenobacter    <NA>
## 57                       Rhodobiaceae        Methyloceanibacter    <NA>
## 58                    Nocardioidaceae               Marmoricola    <NA>
## 59                  Bradyrhizobiaceae            Bradyrhizobium    <NA>
## 60                   Streptococcaceae             Streptococcus    <NA>
## 61                   Lactobacillaceae             Lactobacillus    <NA>
## 62                Sphingobacteriaceae                Pedobacter    <NA>
## 63                     Shewanellaceae                Shewanella    <NA>
## 64                  Brevibacteriaceae            Brevibacterium    <NA>
## 65                     Eubacteriaceae              Anaerofustis    <NA>
## 66                        Gaiellaceae                   Gaiella    <NA>
## 67                 Sphaerobacteraceae             Sphaerobacter    <NA>
## 68                         Thermaceae                   Thermus    <NA>
## 69                 Pseudonocardiaceae         Actinomycetospora    <NA>
## 70                   Beijerinckiaceae              Beijerinckia    <NA>
## 71                    Lachnospiraceae          Clostridium_XlVa    <NA>
## 72                     Micrococcaceae               Micrococcus    <NA>
## 73                   Xanthomonadaceae                Luteimonas    <NA>
## 74                Sphingobacteriaceae          Mucilaginibacter    <NA>
## 75                  Carnobacteriaceae             Catellicoccus    <NA>
## 76                  Bradyrhizobiaceae                    Afipia    <NA>
## 77                      Rikenellaceae                 Alistipes    <NA>
## 78              Peptostreptococcaceae            Clostridium_XI    <NA>
## 79                  Patulibacteraceae              Patulibacter    <NA>
## 80                  Streptomycetaceae              Streptomyces    <NA>
## 81                   Tsukamurellaceae              Tsukamurella    <NA>
## 82               Propionibacteriaceae            Friedmanniella    <NA>
## 83                    Lachnospiraceae             Lactonifactor    <NA>
## 84                   Leuconostocaceae                 Weissella    <NA>
## 85                    Ruminococcaceae            Ethanoligenens    <NA>
## 86                     Bacteroidaceae               Bacteroides    <NA>
## 87                      Bacillaceae_1            Anaerobacillus    <NA>
## 88                   Dermabacteraceae           Brachybacterium    <NA>
## 89                   Rhodobacteraceae             Defluviimonas    <NA>
## 90                   Xanthomonadaceae               Xanthomonas    <NA>
## 91                  Microbacteriaceae             Amnibacterium    <NA>
## 92                  Cellulomonadaceae              Cellulomonas    <NA>
## 93                        Dietziaceae                   Dietzia    <NA>
## 94                   Oxalobacteraceae            Herbaspirillum    <NA>
## 95                  Conexibacteraceae              Conexibacter    <NA>
## 96                     Alcaligenaceae             Achromobacter    <NA>
## 97                       Rhizobiaceae              Neorhizobium    <NA>
## 98                    Ruminococcaceae               Anaerofilum    <NA>
## 99                   Oxalobacteraceae                  Massilia    <NA>
## 100               Erysipelotrichaceae              Turicibacter    <NA>
## 101                Paenibacillaceae_1             Paenibacillus    <NA>
## 102                Pseudonocardiaceae            Pseudonocardia    <NA>
## 103                 Microbacteriaceae            Microbacterium    <NA>
## 104                  Rhodobacteraceae                Paracoccus    <NA>
## 105                 Flavobacteriaceae            Flavobacterium    <NA>
## 106               Methylobacteriaceae                Microvirga    <NA>
## 107                 Sphingomonadaceae           Novosphingobium    <NA>
## 108                   Kineosporiaceae         Pseudokineococcus    <NA>
## 109             Peptostreptococcaceae                Romboutsia    <NA>
## 110                Corynebacteriaceae           Corynebacterium    <NA>
## 111                  Methylocystaceae               Methylopila    <NA>
## 112                    Micrococcaceae              Arthrobacter    <NA>
## 113                 Sphingomonadaceae               Sphingobium    <NA>
## 114               Geodermatophilaceae          Geodermatophilus    <NA>
## 115                  Rhodobacteraceae               Gemmobacter    <NA>
## 116                     Moraxellaceae             Acinetobacter    <NA>
## 117                 Cellulomonadaceae               Actinotalea    <NA>
## 118                    Deinococcaceae               Deinococcus    <NA>
## 119                 Coriobacteriaceae          Denitrobacterium    <NA>
## 120                   Veillonellaceae               Veillonella    <NA>
## 121                 Hyphomicrobiaceae               Rhodoplanes    <NA>
## 122               Geodermatophilaceae              Blastococcus    <NA>
## 123                  Pseudomonadaceae                Cellvibrio    <NA>
## 124   Acidimicrobineae_incertae_sedis           Aciditerrimonas    <NA>
## 125                    Planococcaceae            Lysinibacillus    <NA>
## 126 Clostridiales_Incertae_Sedis_XIII               Anaerovorax    <NA>
## 127                      Nocardiaceae                  Gordonia    <NA>
## 128                 Sanguibacteraceae              Sanguibacter    <NA>
## 129                  Clostridiaceae_1 Clostridium_sensu_stricto    <NA>
## 130                   Ruminococcaceae            Clostridium_IV    <NA>
## 131                 Staphylococcaceae            Staphylococcus    <NA>
## 132                      Brucellaceae              Ochrobactrum    <NA>
## 133                 Aurantimonadaceae                Aureimonas    <NA>
## 134                      Rhizobiaceae                  Shinella    <NA>
## 135                Sphaerobacteraceae               Nitrolancea    <NA>
## 136                 Sphingomonadaceae              Sphingopyxis    <NA>
## 137                  Mycobacteriaceae             Mycobacterium    <NA>
## 138                      Nocardiaceae               Rhodococcus    <NA>
## 139                   Lachnospiraceae             Robinsoniella    <NA>
## 140                 Acidimicrobiaceae             Ilumatobacter    <NA>
## 141                  Caulobacteraceae             Brevundimonas    <NA>
## 142                Intrasporangiaceae                Janibacter    <NA>
## 143                  Burkholderiaceae               Cupriavidus    <NA>
## 144                  Pseudomonadaceae               Pseudomonas    <NA>
## 145                    Eubacteriaceae               Eubacterium    <NA>
## 146                   Ruminococcaceae            Intestinimonas    <NA>
## 147                  Xanthomonadaceae          Stenotrophomonas    <NA>
## 148                 Hyphomicrobiaceae             Pedomicrobium    <NA>
## 149                Enterobacteriaceae                   Pantoea    <NA>
## 150                  Streptococcaceae               Lactococcus    <NA>
## 151               Alicyclobacillaceae              Tumebacillus    <NA>
## 152               Erysipelotrichaceae         Clostridium_XVIII    <NA>
## 153                    Halomonadaceae                 Halomonas    <NA>
## 154                Porphyromonadaceae              Dysgonomonas    <NA>
res.liaG[res.liaG$pval.adj < 0.05,"Feature"]
## [1] "ASV100" "ASV193" "ASV215" "ASV451" "ASV8"
## Three genera sig, represented by these ASVs: "ASV193" "ASV215" "ASV301" "ASV451" "ASV8"

res.ds2G <- DA.ds2(TxO_G, predictor = "Type")
## converting counts to integer mode
## using pre-existing size factors
## estimating dispersions
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates
## fitting model and testing
res.ds2G
##     Feature     baseMean log2FoldChange    lfcSE         stat         pval
## 1     ASV10  33.55412340   -23.62467113 2.672456 -8.840058559           NA
## 2    ASV100   6.07683581    -2.52190026 1.487053 -1.695904368 0.0899039922
## 3   ASV1003   0.00000000             NA       NA           NA           NA
## 4    ASV101   0.60411504    -2.84028417 3.053516 -0.930168329 0.3522839374
## 5   ASV1027   1.50832687     3.99003719 2.744948  1.453592969 0.1460591874
## 6    ASV103  18.95073219     1.99808881 1.557629  1.282776207 0.1995704923
## 7   ASV1046   0.46998886     1.53013308 3.061807  0.499748455 0.6172522090
## 8   ASV1067   0.35283526    -2.14917619 3.073489 -0.699262608 0.4843879305
## 9    ASV107   1.26149544    -3.77445638 2.324120 -1.624036656 0.1043679855
## 10    ASV11  56.62297621     3.56689114 2.109435  1.690922309           NA
## 11  ASV1108   0.21683770    -1.17537336 3.106011 -0.378418959 0.7051193865
## 12  ASV1122   0.20466753    -1.56705870 3.095046 -0.506311977 0.6126376565
## 13   ASV113   0.76873162    -3.15931448 2.569034 -1.229767462 0.2187841960
## 14  ASV1136   1.10468352     1.18524011 2.602815  0.455368488 0.6488441621
## 15  ASV1179   1.35230996     2.49351300 2.365409  1.054157445 0.2918108397
## 16  ASV1184   0.12173394    -1.06653766 3.108225 -0.343133999 0.7314976543
## 17   ASV121   3.08979618    -0.31083650 2.184897 -0.142265941 0.8868699477
## 18  ASV1211   0.17295254    -1.17537336 3.106011 -0.378418959 0.7051193865
## 19  ASV1214   0.21683770    -1.17537336 3.106011 -0.378418959 0.7051193865
## 20  ASV1241   0.00000000             NA       NA           NA           NA
## 21  ASV1262   0.43768241     2.25421139 3.044547  0.740409457 0.4590515825
## 22   ASV129   2.26024130    -4.67806036 2.692111 -1.737691906 0.0822651156
## 23  ASV1318   1.14910298     3.61282560 2.762095  1.308002115 0.1908725921
## 24   ASV134   5.05210010     5.74769083 2.746038  2.093084956           NA
## 25  ASV1382   0.41231161     2.17517854 3.071743  0.708125119 0.4788675618
## 26   ASV139   2.04728484    -3.35090959 2.327969 -1.439413580 0.1500333789
## 27  ASV1397   0.00000000             NA       NA           NA           NA
## 28  ASV1400   0.15350065    -1.30754222 3.102697 -0.421421194 0.6734475455
## 29  ASV1427   0.28755196     1.55532744 3.095982  0.502369592 0.6154075646
## 30  ASV1443   0.00000000             NA       NA           NA           NA
## 31  ASV1470   0.40547437     1.22044087 2.869009  0.425387623 0.6705541274
## 32  ASV1473   0.20398846     1.36619389 3.101227  0.440533333 0.6595508758
## 33  ASV1485   0.00000000             NA       NA           NA           NA
## 34    ASV15   8.65508133    -1.63064142 2.287311 -0.712907740           NA
## 35   ASV155   1.96379347    -4.47563828 2.733845 -1.637122177           NA
## 36  ASV1553   0.32198790     1.50677228 3.097272  0.486483760 0.6266242172
## 37   ASV170   2.82707436     0.01273622 1.850495  0.006882603 0.9945085210
## 38   ASV175   3.06257354     4.49227684 2.790339  1.609939218           NA
## 39   ASV176   1.42200689    -4.01349419 2.724610 -1.473052989 0.1407367483
## 40   ASV177   5.89378025    -0.83750977 1.861003 -0.450031299 0.6526878725
## 41  ASV1787   0.05116688    -0.55854955 3.116540 -0.179221064 0.8577641245
## 42  ASV1814   0.17905951     0.94581366 3.111658  0.303958127 0.7611597922
## 43  ASV1826   0.07056705     0.40323546 3.116540  0.129385636 0.8970525133
## 44  ASV1828   0.20466753    -1.56705870 3.095046 -0.506311977 0.6126376565
## 45   ASV183  15.66783720    -0.68903210 1.526307 -0.451437552 0.6516742234
## 46   ASV185   0.18588155    -1.48403724 3.097635 -0.479087193 0.6318766006
## 47    ASV19  64.93483725     1.28190755 2.036070  0.629599067 0.5289569342
## 48   ASV190   0.70861845    -3.01529528 2.611758 -1.154508042 0.2482919436
## 49  ASV1922   0.32019361     1.79860643 3.088549  0.582346725 0.5603331584
## 50   ASV193   8.02282816     4.90993848 1.690049  2.905204703 0.0036701298
## 51     ASV2 215.14279913    -9.79243542 2.936690 -3.334514748           NA
## 52   ASV204   1.46072281     0.04708302 2.381142  0.019773292 0.9842242236
## 53   ASV207   0.00000000             NA       NA           NA           NA
## 54   ASV214   2.04860575    -4.54008057 2.176958 -2.085515701 0.0370225144
## 55   ASV215   6.42043205     4.98764221 1.700610  2.932855106 0.0033586059
## 56   ASV216   0.76904537    -3.06575485 2.892134 -1.060032183 0.2891299583
## 57  ASV2179   0.25913355     0.94581366 3.111658  0.303958127 0.7611597922
## 58  ASV2184   0.30209366     1.76348282 3.089919  0.570721319 0.5681885648
## 59   ASV221   2.81508052     0.10669045 2.215186  0.048163208 0.9615861717
## 60   ASV223   1.47253411     3.39950770 1.947233  1.745814119 0.0808432568
## 61   ASV226   1.27917209    -3.86321855 3.029787 -1.275079437           NA
## 62    ASV23  49.16573014     4.31248028 2.245197  1.920758423 0.0547621704
## 63   ASV235   1.26643399    -3.77166406 2.539712 -1.485075674 0.1375237791
## 64   ASV236   0.49930229    -2.59610435 2.996379 -0.866413957 0.3862631926
## 65   ASV237   0.00000000             NA       NA           NA           NA
## 66   ASV248   1.56941284     4.05431746 2.496151  1.624227955 0.1043271666
## 67   ASV253   3.52299678     3.02042696 1.647518  1.833319060 0.0667551365
## 68   ASV256   2.51067751     2.19487574 2.619618  0.837860990           NA
## 69   ASV258   0.09294078    -0.94561239 3.110855 -0.303971881 0.7611493135
## 70    ASV26  23.64470916    -1.55336085 1.211976 -1.281676617 0.1999561109
## 71   ASV265   0.72801196    -3.06048199 2.871336 -1.065874038 0.2864805865
## 72   ASV267   5.34767146     2.61165806 2.163767  1.206996161 0.2274336225
## 73   ASV270   2.19078300    -4.63277137 2.729445 -1.697330731           NA
## 74   ASV273   1.42327975    -4.02008581 2.753689 -1.459891079           NA
## 75   ASV274   0.00000000             NA       NA           NA           NA
## 76    ASV29   7.01618800    -0.56669258 2.665635 -0.212591961 0.8316452422
## 77   ASV291   1.00030527    -3.50798716 2.796793 -1.254289109 0.2097369409
## 78   ASV293   0.10841885    -0.55854955 3.116540 -0.179221064 0.8577641245
## 79   ASV296   0.32529271    -2.08537042 3.075833 -0.677985496 0.4977808897
## 80    ASV30  10.65626251    -1.63514014 1.633796 -1.000822812 0.3169124790
## 81   ASV303   1.83080235     2.87325870 2.081087  1.380652965 0.1673856897
## 82   ASV306   1.10149412     1.14435547 2.876145  0.397878171 0.6907199915
## 83    ASV31  15.32688333    -5.31449560 2.117787 -2.509457270 0.0120916844
## 84   ASV311   0.79228199    -3.09567508 2.889758 -1.071257372 0.2840537214
## 85   ASV312   0.40271925    -2.30184438 3.068263 -0.750211006 0.4531276310
## 86   ASV318   1.22294777     3.68742110 2.778546  1.327104644 0.1844740694
## 87   ASV332   4.70776089     1.94784693 1.753388  1.110904859 0.2666093039
## 88   ASV334   0.23235194    -1.70574993 3.090020 -0.552019137 0.5809352417
## 89   ASV337   2.33951637     4.62271165 2.510431  1.841401834 0.0655626943
## 90   ASV338   0.57548046    -2.56577902 2.957970 -0.867412257 0.3857161686
## 91   ASV342   0.00000000             NA       NA           NA           NA
## 92   ASV348   0.97471505    -1.60451888 2.448577 -0.655286321 0.5122834262
## 93   ASV349   1.17152312     3.63085968 2.515186  1.443575080 0.1488585390
## 94   ASV356   0.17941705    -1.38617584 3.100374 -0.447099495 0.6548032234
## 95   ASV359   0.39347757    -2.29931122 3.068345 -0.749365250 0.4536370898
## 96   ASV375   4.90625748    -0.08482477 1.596327 -0.053137471 0.9576223758
## 97   ASV376   0.54863267    -0.78530491 2.792242 -0.281245245 0.7785223044
## 98   ASV378   0.10841885    -0.55854955 3.116540 -0.179221064 0.8577641245
## 99   ASV381   0.66950938    -0.52186129 2.724734 -0.191527456 0.8481123717
## 100  ASV387   0.00000000             NA       NA           NA           NA
## 101  ASV388   0.00000000             NA       NA           NA           NA
## 102  ASV416   1.02449546     3.45533054 2.565667  1.346757023 0.1780585005
## 103   ASV43  12.71567582     0.01201618 1.433067  0.008384939 0.9933098649
## 104   ASV44   8.23767838     0.64202831 1.323556  0.485078418 0.6276207205
## 105  ASV440   0.72115376    -1.61521785 2.722752 -0.593229856 0.5530273347
## 106  ASV445   0.25583442    -1.79864327 3.086891 -0.582671479 0.5601144769
## 107  ASV451   5.90628348     3.65113946 1.729364  2.111261617 0.0347498312
## 108  ASV467   0.00000000             NA       NA           NA           NA
## 109  ASV472   0.92449802     3.30377379 2.551813  1.294676978 0.1954316850
## 110  ASV473   0.10841885    -0.55854955 3.116540 -0.179221064 0.8577641245
## 111  ASV474   0.00000000             NA       NA           NA           NA
## 112  ASV475   0.25018774    -0.55854955 3.116540 -0.179221064 0.8577641245
## 113  ASV483   1.77429907     0.30463173 2.206667  0.138050641 0.8902003952
## 114  ASV506   0.13941116    -1.23437584 3.104868 -0.397561420 0.6909535036
## 115  ASV517   0.93275684    -3.31957710 2.836310 -1.170385657 0.2418458051
## 116  ASV520   0.34077079    -2.11414380 3.074764 -0.687579153 0.4917178400
## 117   ASV53  10.52674255    -6.88094710 2.087893 -3.295640955 0.0009819743
## 118  ASV531   0.64537655    -0.88137672 2.994516 -0.294330276 0.7685055400
## 119  ASV538   0.35816818    -2.19484096 3.071871 -0.714496506 0.4749202159
## 120   ASV54  12.46867021     3.24960170 2.463578  1.319057971 0.1871497326
## 121  ASV558   0.18588155    -1.48403724 3.097635 -0.479087193 0.6318766006
## 122  ASV562   1.19836372     3.67579873 2.511846  1.463385490 0.1433619269
## 123  ASV566   0.53825114    -2.68003332 2.960780 -0.905178057 0.3653710650
## 124  ASV572   0.38465370    -2.24626239 3.070105 -0.731656481 0.4643782649
## 125  ASV585   1.19843671     3.68804837 2.744251  1.343918035 0.1789748933
## 126  ASV586   0.29654831     1.76157347 3.089985  0.570091210 0.5686158369
## 127  ASV588   0.39582360    -1.51017165 3.079481 -0.490398057 0.6238522514
## 128  ASV593   1.61145020     0.63081817 2.419152  0.260760093 0.7942775214
## 129    ASV6  22.25277429    -3.50481711 1.912289 -1.832786275 0.0668343611
## 130   ASV60   5.88038644    -6.03922380 3.008825 -2.007170243           NA
## 131  ASV605   6.31639824     2.66121694 2.389258  1.113825569 0.2653540256
## 132   ASV62   5.99201632    -4.57886532 1.702738 -2.689119731 0.0071640719
## 133  ASV641   0.00000000             NA       NA           NA           NA
## 134  ASV645   0.79215925    -1.04311146 2.446965 -0.426287933 0.6698980498
## 135  ASV647   0.00000000             NA       NA           NA           NA
## 136  ASV652   2.78667212     4.88184545 2.209489  2.209490871 0.0271405167
## 137  ASV665   0.28131967    -1.85962272 3.029108 -0.613917518 0.5392698332
## 138   ASV68  11.08286584     0.54087845 1.454788  0.371791940 0.7100477654
## 139   ASV69   5.09131254     0.83820042 1.745861  0.480107161 0.6311511966
## 140  ASV716   0.24955295     0.46492272 3.111658  0.149413195 0.8812276001
## 141  ASV728   3.36222291     2.73542589 1.912133  1.430562549 0.1525556273
## 142  ASV776   0.30700130    -2.00861822 3.078785 -0.652406063 0.5141392542
## 143  ASV784   0.54435242     2.54789538 2.711277  0.939740042 0.3473509206
## 144  ASV785   0.17295254    -1.17537336 3.106011 -0.378418959 0.7051193865
## 145    ASV8  53.19112654    -4.91092856 1.665842 -2.948016059 0.0031982045
## 146  ASV809   0.40449864     2.07240475 3.076695  0.673581552 0.5005773852
## 147   ASV81   6.20097594     0.68576219 2.278270  0.301001238 0.7634135508
## 148   ASV82   3.26989507    -5.20517981 2.404469 -2.164794007 0.0304034640
## 149  ASV850   0.65466732     2.80924466 2.627681  1.069096655 0.2850261185
## 150   ASV87  10.75846614     2.10878625 1.799299  1.172004293 0.2411953326
## 151    ASV9  38.14244810     0.49638074 2.889078  0.171812882           NA
## 152  ASV906   0.79208884     3.05195736 2.865830  1.064947190 0.2868998284
## 153   ASV91  18.46404374     2.22048307 1.720378  1.290695159 0.1968094039
## 154   ASV95   2.59428813    -4.86090283 2.996436 -1.622227891           NA
## 155  ASV999   0.20224932     0.94581366 3.111658  0.303958127 0.7611597922
##              ordering  pval.adj                     Method  Kingdom
## 1   CloacalSwab>Fecal        NA DESeq2 man. geoMeans (ds2) Bacteria
## 2   CloacalSwab>Fecal 0.6663472 DESeq2 man. geoMeans (ds2) Bacteria
## 3                <NA>        NA DESeq2 man. geoMeans (ds2) Bacteria
## 4   CloacalSwab>Fecal 0.8375052 DESeq2 man. geoMeans (ds2) Bacteria
## 5   Fecal>CloacalSwab 0.6998464 DESeq2 man. geoMeans (ds2) Bacteria
## 6   Fecal>CloacalSwab 0.6998464 DESeq2 man. geoMeans (ds2) Bacteria
## 7   Fecal>CloacalSwab 0.8858022 DESeq2 man. geoMeans (ds2) Bacteria
## 8   CloacalSwab>Fecal 0.8858022 DESeq2 man. geoMeans (ds2) Bacteria
## 9   CloacalSwab>Fecal 0.6921245 DESeq2 man. geoMeans (ds2) Bacteria
## 10  Fecal>CloacalSwab        NA DESeq2 man. geoMeans (ds2) Bacteria
## 11  CloacalSwab>Fecal 0.8858022 DESeq2 man. geoMeans (ds2) Bacteria
## 12  CloacalSwab>Fecal 0.8858022 DESeq2 man. geoMeans (ds2) Bacteria
## 13  CloacalSwab>Fecal 0.7254423 DESeq2 man. geoMeans (ds2) Bacteria
## 14  Fecal>CloacalSwab 0.8858022 DESeq2 man. geoMeans (ds2) Bacteria
## 15  Fecal>CloacalSwab 0.7353633 DESeq2 man. geoMeans (ds2) Bacteria
## 16  CloacalSwab>Fecal 0.8965898 DESeq2 man. geoMeans (ds2) Bacteria
## 17  CloacalSwab>Fecal 0.9341208 DESeq2 man. geoMeans (ds2) Bacteria
## 18  CloacalSwab>Fecal 0.8858022 DESeq2 man. geoMeans (ds2) Bacteria
## 19  CloacalSwab>Fecal 0.8858022 DESeq2 man. geoMeans (ds2) Bacteria
## 20               <NA>        NA DESeq2 man. geoMeans (ds2) Bacteria
## 21  Fecal>CloacalSwab 0.8858022 DESeq2 man. geoMeans (ds2) Bacteria
## 22  CloacalSwab>Fecal 0.6478378 DESeq2 man. geoMeans (ds2) Bacteria
## 23  Fecal>CloacalSwab 0.6998464 DESeq2 man. geoMeans (ds2) Bacteria
## 24  Fecal>CloacalSwab        NA DESeq2 man. geoMeans (ds2) Bacteria
## 25  Fecal>CloacalSwab 0.8858022 DESeq2 man. geoMeans (ds2) Bacteria
## 26  CloacalSwab>Fecal 0.6998464 DESeq2 man. geoMeans (ds2) Bacteria
## 27               <NA>        NA DESeq2 man. geoMeans (ds2) Bacteria
## 28  CloacalSwab>Fecal 0.8858022 DESeq2 man. geoMeans (ds2) Bacteria
## 29  Fecal>CloacalSwab 0.8858022 DESeq2 man. geoMeans (ds2) Bacteria
## 30               <NA>        NA DESeq2 man. geoMeans (ds2) Bacteria
## 31  Fecal>CloacalSwab 0.8858022 DESeq2 man. geoMeans (ds2) Bacteria
## 32  Fecal>CloacalSwab 0.8858022 DESeq2 man. geoMeans (ds2) Bacteria
## 33               <NA>        NA DESeq2 man. geoMeans (ds2) Bacteria
## 34  CloacalSwab>Fecal        NA DESeq2 man. geoMeans (ds2) Bacteria
## 35  CloacalSwab>Fecal        NA DESeq2 man. geoMeans (ds2) Bacteria
## 36  Fecal>CloacalSwab 0.8858022 DESeq2 man. geoMeans (ds2) Bacteria
## 37  Fecal>CloacalSwab 0.9945085 DESeq2 man. geoMeans (ds2) Bacteria
## 38  Fecal>CloacalSwab        NA DESeq2 man. geoMeans (ds2) Bacteria
## 39  CloacalSwab>Fecal 0.6998464 DESeq2 man. geoMeans (ds2) Bacteria
## 40  CloacalSwab>Fecal 0.8858022 DESeq2 man. geoMeans (ds2) Bacteria
## 41  CloacalSwab>Fecal 0.9237460 DESeq2 man. geoMeans (ds2) Bacteria
## 42  Fecal>CloacalSwab 0.8965898 DESeq2 man. geoMeans (ds2) Bacteria
## 43  Fecal>CloacalSwab 0.9341208 DESeq2 man. geoMeans (ds2) Bacteria
## 44  CloacalSwab>Fecal 0.8858022 DESeq2 man. geoMeans (ds2) Bacteria
## 45  CloacalSwab>Fecal 0.8858022 DESeq2 man. geoMeans (ds2) Bacteria
## 46  CloacalSwab>Fecal 0.8858022 DESeq2 man. geoMeans (ds2) Bacteria
## 47  Fecal>CloacalSwab 0.8858022 DESeq2 man. geoMeans (ds2) Bacteria
## 48  CloacalSwab>Fecal 0.7353633 DESeq2 man. geoMeans (ds2) Bacteria
## 49  Fecal>CloacalSwab 0.8858022 DESeq2 man. geoMeans (ds2) Bacteria
## 50  Fecal>CloacalSwab 0.1156091 DESeq2 man. geoMeans (ds2) Bacteria
## 51  CloacalSwab>Fecal        NA DESeq2 man. geoMeans (ds2) Bacteria
## 52  Fecal>CloacalSwab 0.9945085 DESeq2 man. geoMeans (ds2) Bacteria
## 53               <NA>        NA DESeq2 man. geoMeans (ds2) Bacteria
## 54  CloacalSwab>Fecal 0.4664837 DESeq2 man. geoMeans (ds2) Bacteria
## 55  Fecal>CloacalSwab 0.1156091 DESeq2 man. geoMeans (ds2) Bacteria
## 56  CloacalSwab>Fecal 0.7353633 DESeq2 man. geoMeans (ds2) Bacteria
## 57  Fecal>CloacalSwab 0.8965898 DESeq2 man. geoMeans (ds2) Bacteria
## 58  Fecal>CloacalSwab 0.8858022 DESeq2 man. geoMeans (ds2) Bacteria
## 59  Fecal>CloacalSwab 0.9850395 DESeq2 man. geoMeans (ds2) Bacteria
## 60  Fecal>CloacalSwab 0.6478378 DESeq2 man. geoMeans (ds2) Bacteria
## 61  CloacalSwab>Fecal        NA DESeq2 man. geoMeans (ds2) Bacteria
## 62  Fecal>CloacalSwab 0.6015092 DESeq2 man. geoMeans (ds2) Bacteria
## 63  CloacalSwab>Fecal 0.6998464 DESeq2 man. geoMeans (ds2) Bacteria
## 64  CloacalSwab>Fecal 0.8690922 DESeq2 man. geoMeans (ds2) Bacteria
## 65               <NA>        NA DESeq2 man. geoMeans (ds2) Bacteria
## 66  Fecal>CloacalSwab 0.6921245 DESeq2 man. geoMeans (ds2) Bacteria
## 67  Fecal>CloacalSwab 0.6015092 DESeq2 man. geoMeans (ds2) Bacteria
## 68  Fecal>CloacalSwab        NA DESeq2 man. geoMeans (ds2) Bacteria
## 69  CloacalSwab>Fecal 0.8965898 DESeq2 man. geoMeans (ds2) Bacteria
## 70  CloacalSwab>Fecal 0.6998464 DESeq2 man. geoMeans (ds2) Bacteria
## 71  CloacalSwab>Fecal 0.7353633 DESeq2 man. geoMeans (ds2) Bacteria
## 72  Fecal>CloacalSwab 0.7347855 DESeq2 man. geoMeans (ds2) Bacteria
## 73  CloacalSwab>Fecal        NA DESeq2 man. geoMeans (ds2) Bacteria
## 74  CloacalSwab>Fecal        NA DESeq2 man. geoMeans (ds2) Bacteria
## 75               <NA>        NA DESeq2 man. geoMeans (ds2) Bacteria
## 76  CloacalSwab>Fecal 0.9237460 DESeq2 man. geoMeans (ds2) Bacteria
## 77  CloacalSwab>Fecal 0.7142393 DESeq2 man. geoMeans (ds2) Bacteria
## 78  CloacalSwab>Fecal 0.9237460 DESeq2 man. geoMeans (ds2) Bacteria
## 79  CloacalSwab>Fecal 0.8858022 DESeq2 man. geoMeans (ds2) Bacteria
## 80  CloacalSwab>Fecal 0.7829602 DESeq2 man. geoMeans (ds2) Bacteria
## 81  Fecal>CloacalSwab 0.6998464 DESeq2 man. geoMeans (ds2) Bacteria
## 82  Fecal>CloacalSwab 0.8858022 DESeq2 man. geoMeans (ds2) Bacteria
## 83  CloacalSwab>Fecal 0.2539254 DESeq2 man. geoMeans (ds2) Bacteria
## 84  CloacalSwab>Fecal 0.7353633 DESeq2 man. geoMeans (ds2) Bacteria
## 85  CloacalSwab>Fecal 0.8858022 DESeq2 man. geoMeans (ds2) Bacteria
## 86  Fecal>CloacalSwab 0.6998464 DESeq2 man. geoMeans (ds2) Bacteria
## 87  Fecal>CloacalSwab 0.7353633 DESeq2 man. geoMeans (ds2) Bacteria
## 88  CloacalSwab>Fecal 0.8858022 DESeq2 man. geoMeans (ds2) Bacteria
## 89  Fecal>CloacalSwab 0.6015092 DESeq2 man. geoMeans (ds2) Bacteria
## 90  CloacalSwab>Fecal 0.8690922 DESeq2 man. geoMeans (ds2) Bacteria
## 91               <NA>        NA DESeq2 man. geoMeans (ds2) Bacteria
## 92  CloacalSwab>Fecal 0.8858022 DESeq2 man. geoMeans (ds2) Bacteria
## 93  Fecal>CloacalSwab 0.6998464 DESeq2 man. geoMeans (ds2) Bacteria
## 94  CloacalSwab>Fecal 0.8858022 DESeq2 man. geoMeans (ds2) Bacteria
## 95  CloacalSwab>Fecal 0.8858022 DESeq2 man. geoMeans (ds2) Bacteria
## 96  CloacalSwab>Fecal 0.9850395 DESeq2 man. geoMeans (ds2) Bacteria
## 97  CloacalSwab>Fecal 0.8999432 DESeq2 man. geoMeans (ds2) Bacteria
## 98  CloacalSwab>Fecal 0.9237460 DESeq2 man. geoMeans (ds2) Bacteria
## 99  CloacalSwab>Fecal 0.9237460 DESeq2 man. geoMeans (ds2) Bacteria
## 100              <NA>        NA DESeq2 man. geoMeans (ds2) Bacteria
## 101              <NA>        NA DESeq2 man. geoMeans (ds2) Bacteria
## 102 Fecal>CloacalSwab 0.6998464 DESeq2 man. geoMeans (ds2) Bacteria
## 103 Fecal>CloacalSwab 0.9945085 DESeq2 man. geoMeans (ds2) Bacteria
## 104 Fecal>CloacalSwab 0.8858022 DESeq2 man. geoMeans (ds2) Bacteria
## 105 CloacalSwab>Fecal 0.8858022 DESeq2 man. geoMeans (ds2) Bacteria
## 106 CloacalSwab>Fecal 0.8858022 DESeq2 man. geoMeans (ds2) Bacteria
## 107 Fecal>CloacalSwab 0.4664837 DESeq2 man. geoMeans (ds2) Bacteria
## 108              <NA>        NA DESeq2 man. geoMeans (ds2) Bacteria
## 109 Fecal>CloacalSwab 0.6998464 DESeq2 man. geoMeans (ds2) Bacteria
## 110 CloacalSwab>Fecal 0.9237460 DESeq2 man. geoMeans (ds2) Bacteria
## 111              <NA>        NA DESeq2 man. geoMeans (ds2) Bacteria
## 112 CloacalSwab>Fecal 0.9237460 DESeq2 man. geoMeans (ds2) Bacteria
## 113 Fecal>CloacalSwab 0.9341208 DESeq2 man. geoMeans (ds2) Bacteria
## 114 CloacalSwab>Fecal 0.8858022 DESeq2 man. geoMeans (ds2) Bacteria
## 115 CloacalSwab>Fecal 0.7353633 DESeq2 man. geoMeans (ds2) Bacteria
## 116 CloacalSwab>Fecal 0.8858022 DESeq2 man. geoMeans (ds2) Bacteria
## 117 CloacalSwab>Fecal 0.1156091 DESeq2 man. geoMeans (ds2) Bacteria
## 118 CloacalSwab>Fecal 0.8965898 DESeq2 man. geoMeans (ds2) Bacteria
## 119 CloacalSwab>Fecal 0.8858022 DESeq2 man. geoMeans (ds2) Bacteria
## 120 Fecal>CloacalSwab 0.6998464 DESeq2 man. geoMeans (ds2) Bacteria
## 121 CloacalSwab>Fecal 0.8858022 DESeq2 man. geoMeans (ds2) Bacteria
## 122 Fecal>CloacalSwab 0.6998464 DESeq2 man. geoMeans (ds2) Bacteria
## 123 CloacalSwab>Fecal 0.8525325 DESeq2 man. geoMeans (ds2) Bacteria
## 124 CloacalSwab>Fecal 0.8858022 DESeq2 man. geoMeans (ds2) Bacteria
## 125 Fecal>CloacalSwab 0.6998464 DESeq2 man. geoMeans (ds2) Bacteria
## 126 Fecal>CloacalSwab 0.8858022 DESeq2 man. geoMeans (ds2) Bacteria
## 127 CloacalSwab>Fecal 0.8858022 DESeq2 man. geoMeans (ds2) Bacteria
## 128 Fecal>CloacalSwab 0.9098088 DESeq2 man. geoMeans (ds2) Bacteria
## 129 CloacalSwab>Fecal 0.6015092 DESeq2 man. geoMeans (ds2) Bacteria
## 130 CloacalSwab>Fecal        NA DESeq2 man. geoMeans (ds2) Bacteria
## 131 Fecal>CloacalSwab 0.7353633 DESeq2 man. geoMeans (ds2) Bacteria
## 132 CloacalSwab>Fecal 0.1805346 DESeq2 man. geoMeans (ds2) Bacteria
## 133              <NA>        NA DESeq2 man. geoMeans (ds2) Bacteria
## 134 CloacalSwab>Fecal 0.8858022 DESeq2 man. geoMeans (ds2) Bacteria
## 135              <NA>        NA DESeq2 man. geoMeans (ds2) Bacteria
## 136 Fecal>CloacalSwab 0.4664837 DESeq2 man. geoMeans (ds2) Bacteria
## 137 CloacalSwab>Fecal 0.8858022 DESeq2 man. geoMeans (ds2) Bacteria
## 138 Fecal>CloacalSwab 0.8858022 DESeq2 man. geoMeans (ds2) Bacteria
## 139 Fecal>CloacalSwab 0.8858022 DESeq2 man. geoMeans (ds2) Bacteria
## 140 Fecal>CloacalSwab 0.9341208 DESeq2 man. geoMeans (ds2) Bacteria
## 141 Fecal>CloacalSwab 0.6998464 DESeq2 man. geoMeans (ds2) Bacteria
## 142 CloacalSwab>Fecal 0.8858022 DESeq2 man. geoMeans (ds2) Bacteria
## 143 Fecal>CloacalSwab 0.8375052 DESeq2 man. geoMeans (ds2) Bacteria
## 144 CloacalSwab>Fecal 0.8858022 DESeq2 man. geoMeans (ds2) Bacteria
## 145 CloacalSwab>Fecal 0.1156091 DESeq2 man. geoMeans (ds2) Bacteria
## 146 Fecal>CloacalSwab 0.8858022 DESeq2 man. geoMeans (ds2) Bacteria
## 147 Fecal>CloacalSwab 0.8965898 DESeq2 man. geoMeans (ds2) Bacteria
## 148 CloacalSwab>Fecal 0.4664837 DESeq2 man. geoMeans (ds2) Bacteria
## 149 Fecal>CloacalSwab 0.7353633 DESeq2 man. geoMeans (ds2) Bacteria
## 150 Fecal>CloacalSwab 0.7353633 DESeq2 man. geoMeans (ds2) Bacteria
## 151 Fecal>CloacalSwab        NA DESeq2 man. geoMeans (ds2) Bacteria
## 152 Fecal>CloacalSwab 0.7353633 DESeq2 man. geoMeans (ds2) Bacteria
## 153 Fecal>CloacalSwab 0.6998464 DESeq2 man. geoMeans (ds2) Bacteria
## 154 CloacalSwab>Fecal        NA DESeq2 man. geoMeans (ds2) Bacteria
## 155 Fecal>CloacalSwab 0.8965898 DESeq2 man. geoMeans (ds2) Bacteria
##                  Phylum               Class               Order
## 1        Proteobacteria Gammaproteobacteria   Oceanospirillales
## 2        Proteobacteria Alphaproteobacteria         Rhizobiales
## 3        Actinobacteria      Actinobacteria     Actinomycetales
## 4         Bacteroidetes    Sphingobacteriia  Sphingobacteriales
## 5        Proteobacteria Alphaproteobacteria         Rhizobiales
## 6        Actinobacteria      Actinobacteria Solirubrobacterales
## 7        Actinobacteria      Actinobacteria     Actinomycetales
## 8        Proteobacteria  Betaproteobacteria     Burkholderiales
## 9            Firmicutes             Bacilli     Lactobacillales
## 10       Proteobacteria Gammaproteobacteria   Enterobacteriales
## 11        Bacteroidetes         Bacteroidia       Bacteroidales
## 12         Fusobacteria       Fusobacteriia     Fusobacteriales
## 13        Bacteroidetes      Flavobacteriia    Flavobacteriales
## 14       Actinobacteria      Actinobacteria    Acidimicrobiales
## 15       Actinobacteria      Actinobacteria     Actinomycetales
## 16        Bacteroidetes          Cytophagia        Cytophagales
## 17       Actinobacteria      Actinobacteria     Actinomycetales
## 18        Bacteroidetes      Flavobacteriia    Flavobacteriales
## 19       Proteobacteria Alphaproteobacteria         Rhizobiales
## 20       Actinobacteria      Actinobacteria   Bifidobacteriales
## 21       Proteobacteria Alphaproteobacteria         Rhizobiales
## 22       Proteobacteria  Betaproteobacteria     Burkholderiales
## 23       Actinobacteria      Actinobacteria     Actinomycetales
## 24           Firmicutes       Negativicutes     Selenomonadales
## 25       Actinobacteria      Actinobacteria     Actinomycetales
## 26       Proteobacteria Alphaproteobacteria         Rhizobiales
## 27       Proteobacteria Alphaproteobacteria     Caulobacterales
## 28        Bacteroidetes         Bacteroidia       Bacteroidales
## 29          Nitrospirae          Nitrospira       Nitrospirales
## 30       Actinobacteria      Actinobacteria     Actinomycetales
## 31          Chloroflexi        Chloroflexia       Kallotenuales
## 32       Proteobacteria Deltaproteobacteria        Myxococcales
## 33       Actinobacteria      Actinobacteria     Actinomycetales
## 34       Proteobacteria Gammaproteobacteria   Enterobacteriales
## 35       Proteobacteria  Betaproteobacteria     Burkholderiales
## 36       Proteobacteria Alphaproteobacteria     Rhodobacterales
## 37       Actinobacteria      Actinobacteria     Actinomycetales
## 38       Proteobacteria Deltaproteobacteria  Desulfovibrionales
## 39       Actinobacteria      Actinobacteria     Actinomycetales
## 40           Firmicutes             Bacilli          Bacillales
## 41       Proteobacteria  Betaproteobacteria     Burkholderiales
## 42       Planctomycetes      Planctomycetia    Planctomycetales
## 43       Actinobacteria      Actinobacteria    Acidimicrobiales
## 44     Gemmatimonadetes    Gemmatimonadetes    Gemmatimonadales
## 45       Actinobacteria      Actinobacteria     Actinomycetales
## 46           Firmicutes             Bacilli          Bacillales
## 47           Firmicutes             Bacilli     Lactobacillales
## 48       Actinobacteria      Actinobacteria     Actinomycetales
## 49       Proteobacteria Deltaproteobacteria        Myxococcales
## 50       Actinobacteria      Actinobacteria     Rubrobacterales
## 51       Proteobacteria Gammaproteobacteria       Legionellales
## 52       Actinobacteria      Actinobacteria     Actinomycetales
## 53       Proteobacteria Gammaproteobacteria   Enterobacteriales
## 54       Proteobacteria Alphaproteobacteria    Sphingomonadales
## 55       Actinobacteria      Actinobacteria     Actinomycetales
## 56        Bacteroidetes          Cytophagia        Cytophagales
## 57       Proteobacteria Alphaproteobacteria         Rhizobiales
## 58           Firmicutes          Clostridia       Clostridiales
## 59       Actinobacteria      Actinobacteria     Actinomycetales
## 60       Proteobacteria Alphaproteobacteria         Rhizobiales
## 61           Firmicutes             Bacilli     Lactobacillales
## 62           Firmicutes             Bacilli     Lactobacillales
## 63        Bacteroidetes    Sphingobacteriia  Sphingobacteriales
## 64       Proteobacteria Gammaproteobacteria     Alteromonadales
## 65       Actinobacteria      Actinobacteria     Actinomycetales
## 66           Firmicutes          Clostridia       Clostridiales
## 67       Actinobacteria      Actinobacteria          Gaiellales
## 68          Chloroflexi      Thermomicrobia   Sphaerobacterales
## 69  Deinococcus-Thermus          Deinococci           Thermales
## 70       Actinobacteria      Actinobacteria     Actinomycetales
## 71       Proteobacteria Alphaproteobacteria         Rhizobiales
## 72           Firmicutes          Clostridia       Clostridiales
## 73       Actinobacteria      Actinobacteria     Actinomycetales
## 74       Proteobacteria Gammaproteobacteria     Xanthomonadales
## 75        Bacteroidetes    Sphingobacteriia  Sphingobacteriales
## 76           Firmicutes             Bacilli     Lactobacillales
## 77       Proteobacteria Alphaproteobacteria         Rhizobiales
## 78        Bacteroidetes         Bacteroidia       Bacteroidales
## 79           Firmicutes          Clostridia       Clostridiales
## 80       Actinobacteria      Actinobacteria Solirubrobacterales
## 81       Actinobacteria      Actinobacteria     Actinomycetales
## 82       Actinobacteria      Actinobacteria     Actinomycetales
## 83       Actinobacteria      Actinobacteria     Actinomycetales
## 84           Firmicutes          Clostridia       Clostridiales
## 85           Firmicutes             Bacilli     Lactobacillales
## 86           Firmicutes          Clostridia       Clostridiales
## 87        Bacteroidetes         Bacteroidia       Bacteroidales
## 88           Firmicutes             Bacilli          Bacillales
## 89       Actinobacteria      Actinobacteria     Actinomycetales
## 90       Proteobacteria Alphaproteobacteria     Rhodobacterales
## 91       Proteobacteria Gammaproteobacteria     Xanthomonadales
## 92       Actinobacteria      Actinobacteria     Actinomycetales
## 93       Actinobacteria      Actinobacteria     Actinomycetales
## 94       Actinobacteria      Actinobacteria     Actinomycetales
## 95       Proteobacteria  Betaproteobacteria     Burkholderiales
## 96       Actinobacteria      Actinobacteria Solirubrobacterales
## 97       Proteobacteria  Betaproteobacteria     Burkholderiales
## 98       Proteobacteria Alphaproteobacteria         Rhizobiales
## 99           Firmicutes          Clostridia       Clostridiales
## 100      Proteobacteria  Betaproteobacteria     Burkholderiales
## 101          Firmicutes    Erysipelotrichia  Erysipelotrichales
## 102          Firmicutes             Bacilli          Bacillales
## 103      Actinobacteria      Actinobacteria     Actinomycetales
## 104      Actinobacteria      Actinobacteria     Actinomycetales
## 105      Proteobacteria Alphaproteobacteria     Rhodobacterales
## 106       Bacteroidetes      Flavobacteriia    Flavobacteriales
## 107      Proteobacteria Alphaproteobacteria         Rhizobiales
## 108      Proteobacteria Alphaproteobacteria    Sphingomonadales
## 109      Actinobacteria      Actinobacteria     Actinomycetales
## 110          Firmicutes          Clostridia       Clostridiales
## 111      Actinobacteria      Actinobacteria     Actinomycetales
## 112      Proteobacteria Alphaproteobacteria         Rhizobiales
## 113      Actinobacteria      Actinobacteria     Actinomycetales
## 114      Proteobacteria Alphaproteobacteria    Sphingomonadales
## 115      Actinobacteria      Actinobacteria     Actinomycetales
## 116      Proteobacteria Alphaproteobacteria     Rhodobacterales
## 117      Proteobacteria Gammaproteobacteria     Pseudomonadales
## 118      Actinobacteria      Actinobacteria     Actinomycetales
## 119 Deinococcus-Thermus          Deinococci       Deinococcales
## 120      Actinobacteria      Actinobacteria    Coriobacteriales
## 121          Firmicutes       Negativicutes     Selenomonadales
## 122      Proteobacteria Alphaproteobacteria         Rhizobiales
## 123      Actinobacteria      Actinobacteria     Actinomycetales
## 124      Proteobacteria Gammaproteobacteria     Pseudomonadales
## 125      Actinobacteria      Actinobacteria    Acidimicrobiales
## 126          Firmicutes             Bacilli          Bacillales
## 127          Firmicutes          Clostridia       Clostridiales
## 128      Actinobacteria      Actinobacteria     Actinomycetales
## 129      Actinobacteria      Actinobacteria     Actinomycetales
## 130          Firmicutes          Clostridia       Clostridiales
## 131          Firmicutes          Clostridia       Clostridiales
## 132          Firmicutes             Bacilli          Bacillales
## 133      Proteobacteria Alphaproteobacteria         Rhizobiales
## 134      Proteobacteria Alphaproteobacteria         Rhizobiales
## 135      Proteobacteria Alphaproteobacteria         Rhizobiales
## 136         Chloroflexi      Thermomicrobia   Sphaerobacterales
## 137      Proteobacteria Alphaproteobacteria    Sphingomonadales
## 138      Actinobacteria      Actinobacteria     Actinomycetales
## 139      Actinobacteria      Actinobacteria     Actinomycetales
## 140          Firmicutes          Clostridia       Clostridiales
## 141      Actinobacteria      Actinobacteria    Acidimicrobiales
## 142      Proteobacteria Alphaproteobacteria     Caulobacterales
## 143      Actinobacteria      Actinobacteria     Actinomycetales
## 144      Proteobacteria  Betaproteobacteria     Burkholderiales
## 145      Proteobacteria Gammaproteobacteria     Pseudomonadales
## 146          Firmicutes          Clostridia       Clostridiales
## 147          Firmicutes          Clostridia       Clostridiales
## 148      Proteobacteria Gammaproteobacteria     Xanthomonadales
## 149      Proteobacteria Alphaproteobacteria         Rhizobiales
## 150      Proteobacteria Gammaproteobacteria   Enterobacteriales
## 151          Firmicutes             Bacilli     Lactobacillales
## 152          Firmicutes             Bacilli          Bacillales
## 153          Firmicutes    Erysipelotrichia  Erysipelotrichales
## 154      Proteobacteria Gammaproteobacteria   Oceanospirillales
## 155       Bacteroidetes         Bacteroidia       Bacteroidales
##                                Family                     Genus Species
## 1                      Halomonadaceae                Salinicola    <NA>
## 2                 Methylobacteriaceae          Methylobacterium    <NA>
## 3                      Micrococcaceae                   Kocuria    <NA>
## 4                 Sphingobacteriaceae          Sphingobacterium    <NA>
## 5                  Phyllobacteriaceae             Mesorhizobium    <NA>
## 6                Solirubrobacteraceae           Solirubrobacter    <NA>
## 7                  Micromonosporaceae                    Asanoa    <NA>
## 8                      Comamonadaceae                Acidovorax    <NA>
## 9                   Carnobacteriaceae            Carnobacterium    <NA>
## 10                 Enterobacteriaceae              Buttiauxella    <NA>
## 11                 Porphyromonadaceae           Parabacteroides    <NA>
## 12                   Fusobacteriaceae             Fusobacterium    <NA>
## 13                  Flavobacteriaceae          Chryseobacterium    <NA>
## 14                          Iamiaceae                     Iamia    <NA>
## 15               Propionibacteriaceae         Mariniluteicoccus    <NA>
## 16                      Cytophagaceae               Dyadobacter    <NA>
## 17                  Microbacteriaceae                Agrococcus    <NA>
## 18                  Flavobacteriaceae          Leeuwenhoekiella    <NA>
## 19                  Bradyrhizobiaceae                     Bosea    <NA>
## 20                 Bifidobacteriaceae           Bifidobacterium    <NA>
## 21                  Hyphomicrobiaceae            Hyphomicrobium    <NA>
## 22                     Comamonadaceae                   Delftia    <NA>
## 23                 Micromonosporaceae              Actinoplanes    <NA>
## 24                    Veillonellaceae                 Pelosinus    <NA>
## 25                    Acidothermaceae              Acidothermus    <NA>
## 26                       Rhizobiaceae                 Rhizobium    <NA>
## 27                   Caulobacteraceae               Caulobacter    <NA>
## 28                     Prevotellaceae                Prevotella    <NA>
## 29                     Nitrospiraceae                Nitrospira    <NA>
## 30                     Micrococcaceae                    Rothia    <NA>
## 31                     Kallotenuaceae                Kallotenue    <NA>
## 32                   Labilitrichaceae               Labilithrix    <NA>
## 33                  Microbacteriaceae                 Leifsonia    <NA>
## 34                 Enterobacteriaceae              Enterobacter    <NA>
## 35                   Burkholderiaceae                 Ralstonia    <NA>
## 36                   Rhodobacteraceae               Amaricoccus    <NA>
## 37                  Microbacteriaceae            Curtobacterium    <NA>
## 38                Desulfovibrionaceae             Desulfovibrio    <NA>
## 39               Propionibacteriaceae         Propionibacterium    <NA>
## 40                      Bacillaceae_1                  Bacillus    <NA>
## 41                     Comamonadaceae                 Comamonas    <NA>
## 42                  Planctomycetaceae                   Gemmata    <NA>
## 43                          Iamiaceae              Aquihabitans    <NA>
## 44                  Gemmatimonadaceae              Gemmatimonas    <NA>
## 45                    Nocardioidaceae              Nocardioides    <NA>
## 46       Bacillales_Incertae_Sedis_XI                   Gemella    <NA>
## 47                    Enterococcaceae              Enterococcus    <NA>
## 48                  Microbacteriaceae         Pseudoclavibacter    <NA>
## 49                      Myxococcaceae                Myxococcus    <NA>
## 50                   Rubrobacteraceae               Rubrobacter    <NA>
## 51                       Coxiellaceae           Diplorickettsia    <NA>
## 52                       Nocardiaceae                Williamsia    <NA>
## 53                 Enterobacteriaceae                  Serratia    <NA>
## 54                  Sphingomonadaceae              Sphingomonas    <NA>
## 55               Propionibacteriaceae              Microlunatus    <NA>
## 56                      Cytophagaceae              Hymenobacter    <NA>
## 57                       Rhodobiaceae        Methyloceanibacter    <NA>
## 58                    Ruminococcaceae       Acetanaerobacterium    <NA>
## 59                    Nocardioidaceae               Marmoricola    <NA>
## 60                  Bradyrhizobiaceae            Bradyrhizobium    <NA>
## 61                   Streptococcaceae             Streptococcus    <NA>
## 62                   Lactobacillaceae             Lactobacillus    <NA>
## 63                Sphingobacteriaceae                Pedobacter    <NA>
## 64                     Shewanellaceae                Shewanella    <NA>
## 65                  Brevibacteriaceae            Brevibacterium    <NA>
## 66                     Eubacteriaceae              Anaerofustis    <NA>
## 67                        Gaiellaceae                   Gaiella    <NA>
## 68                 Sphaerobacteraceae             Sphaerobacter    <NA>
## 69                         Thermaceae                   Thermus    <NA>
## 70                 Pseudonocardiaceae         Actinomycetospora    <NA>
## 71                   Beijerinckiaceae              Beijerinckia    <NA>
## 72                    Lachnospiraceae          Clostridium_XlVa    <NA>
## 73                     Micrococcaceae               Micrococcus    <NA>
## 74                   Xanthomonadaceae                Luteimonas    <NA>
## 75                Sphingobacteriaceae          Mucilaginibacter    <NA>
## 76                  Carnobacteriaceae             Catellicoccus    <NA>
## 77                  Bradyrhizobiaceae                    Afipia    <NA>
## 78                      Rikenellaceae                 Alistipes    <NA>
## 79              Peptostreptococcaceae            Clostridium_XI    <NA>
## 80                  Patulibacteraceae              Patulibacter    <NA>
## 81                  Streptomycetaceae              Streptomyces    <NA>
## 82                   Tsukamurellaceae              Tsukamurella    <NA>
## 83               Propionibacteriaceae            Friedmanniella    <NA>
## 84                    Lachnospiraceae             Lactonifactor    <NA>
## 85                   Leuconostocaceae                 Weissella    <NA>
## 86                    Ruminococcaceae            Ethanoligenens    <NA>
## 87                     Bacteroidaceae               Bacteroides    <NA>
## 88                      Bacillaceae_1            Anaerobacillus    <NA>
## 89                   Dermabacteraceae           Brachybacterium    <NA>
## 90                   Rhodobacteraceae             Defluviimonas    <NA>
## 91                   Xanthomonadaceae               Xanthomonas    <NA>
## 92                  Microbacteriaceae             Amnibacterium    <NA>
## 93                  Cellulomonadaceae              Cellulomonas    <NA>
## 94                        Dietziaceae                   Dietzia    <NA>
## 95                   Oxalobacteraceae            Herbaspirillum    <NA>
## 96                  Conexibacteraceae              Conexibacter    <NA>
## 97                     Alcaligenaceae             Achromobacter    <NA>
## 98                       Rhizobiaceae              Neorhizobium    <NA>
## 99                    Ruminococcaceae               Anaerofilum    <NA>
## 100                  Oxalobacteraceae                  Massilia    <NA>
## 101               Erysipelotrichaceae              Turicibacter    <NA>
## 102                Paenibacillaceae_1             Paenibacillus    <NA>
## 103                Pseudonocardiaceae            Pseudonocardia    <NA>
## 104                 Microbacteriaceae            Microbacterium    <NA>
## 105                  Rhodobacteraceae                Paracoccus    <NA>
## 106                 Flavobacteriaceae            Flavobacterium    <NA>
## 107               Methylobacteriaceae                Microvirga    <NA>
## 108                 Sphingomonadaceae           Novosphingobium    <NA>
## 109                   Kineosporiaceae         Pseudokineococcus    <NA>
## 110             Peptostreptococcaceae                Romboutsia    <NA>
## 111                Corynebacteriaceae           Corynebacterium    <NA>
## 112                  Methylocystaceae               Methylopila    <NA>
## 113                    Micrococcaceae              Arthrobacter    <NA>
## 114                 Sphingomonadaceae               Sphingobium    <NA>
## 115               Geodermatophilaceae          Geodermatophilus    <NA>
## 116                  Rhodobacteraceae               Gemmobacter    <NA>
## 117                     Moraxellaceae             Acinetobacter    <NA>
## 118                 Cellulomonadaceae               Actinotalea    <NA>
## 119                    Deinococcaceae               Deinococcus    <NA>
## 120                 Coriobacteriaceae          Denitrobacterium    <NA>
## 121                   Veillonellaceae               Veillonella    <NA>
## 122                 Hyphomicrobiaceae               Rhodoplanes    <NA>
## 123               Geodermatophilaceae              Blastococcus    <NA>
## 124                  Pseudomonadaceae                Cellvibrio    <NA>
## 125   Acidimicrobineae_incertae_sedis           Aciditerrimonas    <NA>
## 126                    Planococcaceae            Lysinibacillus    <NA>
## 127 Clostridiales_Incertae_Sedis_XIII               Anaerovorax    <NA>
## 128                      Nocardiaceae                  Gordonia    <NA>
## 129                 Sanguibacteraceae              Sanguibacter    <NA>
## 130                  Clostridiaceae_1 Clostridium_sensu_stricto    <NA>
## 131                   Ruminococcaceae            Clostridium_IV    <NA>
## 132                 Staphylococcaceae            Staphylococcus    <NA>
## 133                      Brucellaceae              Ochrobactrum    <NA>
## 134                 Aurantimonadaceae                Aureimonas    <NA>
## 135                      Rhizobiaceae                  Shinella    <NA>
## 136                Sphaerobacteraceae               Nitrolancea    <NA>
## 137                 Sphingomonadaceae              Sphingopyxis    <NA>
## 138                  Mycobacteriaceae             Mycobacterium    <NA>
## 139                      Nocardiaceae               Rhodococcus    <NA>
## 140                   Lachnospiraceae             Robinsoniella    <NA>
## 141                 Acidimicrobiaceae             Ilumatobacter    <NA>
## 142                  Caulobacteraceae             Brevundimonas    <NA>
## 143                Intrasporangiaceae                Janibacter    <NA>
## 144                  Burkholderiaceae               Cupriavidus    <NA>
## 145                  Pseudomonadaceae               Pseudomonas    <NA>
## 146                    Eubacteriaceae               Eubacterium    <NA>
## 147                   Ruminococcaceae            Intestinimonas    <NA>
## 148                  Xanthomonadaceae          Stenotrophomonas    <NA>
## 149                 Hyphomicrobiaceae             Pedomicrobium    <NA>
## 150                Enterobacteriaceae                   Pantoea    <NA>
## 151                  Streptococcaceae               Lactococcus    <NA>
## 152               Alicyclobacillaceae              Tumebacillus    <NA>
## 153               Erysipelotrichaceae         Clostridium_XVIII    <NA>
## 154                    Halomonadaceae                 Halomonas    <NA>
## 155                Porphyromonadaceae              Dysgonomonas    <NA>
res.ds2G[res.ds2G$pval.adj < 0.05,"Feature"]
##  [1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
## [24] NA NA NA NA NA NA
## Nothing with ds2...hmmm... 

featurePlot(TxO_G, predictor = "Type", feature = "ASV8") + theme_classic()

featurePlot(TxO_G, predictor = "Type", feature = "ASV193") + theme_classic()

featurePlot(TxO_G, predictor = "Type", feature = "ASV215") + theme_classic()

## These plots do show differences between sample types at the genus level. Would report

## last phylum level 


TxO_P <- tax_glom(TxO, taxrank = "Phylum")


TxO_P
## phyloseq-class experiment-level object
## otu_table()   OTU Table:         [ 13 taxa and 12 samples ]
## sample_data() Sample Data:       [ 12 samples by 21 sample variables ]
## tax_table()   Taxonomy Table:    [ 13 taxa by 7 taxonomic ranks ]
## refseq()      DNAStringSet:      [ 13 reference sequences ]
## Testing 13 phyla

res.liaP <- DA.lia(TxO_P, predictor = "Type")
## Warning: Zero sample variances detected, have been offset away from zero
res.liaP
##    Feature      logFC    AveExpr          t        pval   pval.adj
## 1  ASV1122  0.0000000  0.0000000  0.0000000 1.000000000 1.00000000
## 2  ASV1133  1.4664121  0.5018161  3.2956415 0.007470802 0.06052890
## 3  ASV1427  0.3446892 -0.0578554  1.3740281 0.197759349 0.33901603
## 4  ASV1814  0.2291647 -0.1156177  1.0203199 0.330275591 0.43965824
## 5     ASV2 -1.0178976  5.3144260 -2.1434962 0.056155269 0.16846581
## 6    ASV24  0.2553467  3.3587654  0.2477682 0.809042583 0.88259191
## 7   ASV256  2.1045247  1.3199905  2.8663987 0.015858915 0.06343566
## 8   ASV332 -0.7954141  1.6431743 -1.1872599 0.261023085 0.39153463
## 9   ASV538 -0.2077745  0.1038872 -1.5919540 0.140720644 0.28144129
## 10    ASV6  0.3843566  5.3276197  0.9435603 0.366381870 0.43965824
## 11  ASV806  1.1104825  0.6226485  1.9395357 0.079470144 0.19072835
## 12    ASV9  1.5148381  5.0950255  3.1237948 0.010088150 0.06052890
##            B          ordering            Method  Kingdom
## 1  -5.958500              <NA> LIMMA - ALR (lia) Bacteria
## 2  -2.242701 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 3  -5.075024 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 4  -5.452306 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 5  -4.032037 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 6  -5.927207 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 7  -2.916452 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 8  -5.284627 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 9  -4.805133 CloacalSwab>Fecal LIMMA - ALR (lia) Bacteria
## 10 -5.522540 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 11 -4.329969 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
## 12 -2.511772 Fecal>CloacalSwab LIMMA - ALR (lia) Bacteria
##                       Phylum Class Order Family Genus Species
## 1               Fusobacteria  <NA>  <NA>   <NA>  <NA>    <NA>
## 2              Acidobacteria  <NA>  <NA>   <NA>  <NA>    <NA>
## 3                Nitrospirae  <NA>  <NA>   <NA>  <NA>    <NA>
## 4             Planctomycetes  <NA>  <NA>   <NA>  <NA>    <NA>
## 5             Proteobacteria  <NA>  <NA>   <NA>  <NA>    <NA>
## 6  Cyanobacteria/Chloroplast  <NA>  <NA>   <NA>  <NA>    <NA>
## 7                Chloroflexi  <NA>  <NA>   <NA>  <NA>    <NA>
## 8              Bacteroidetes  <NA>  <NA>   <NA>  <NA>    <NA>
## 9        Deinococcus-Thermus  <NA>  <NA>   <NA>  <NA>    <NA>
## 10            Actinobacteria  <NA>  <NA>   <NA>  <NA>    <NA>
## 11           Verrucomicrobia  <NA>  <NA>   <NA>  <NA>    <NA>
## 12                Firmicutes  <NA>  <NA>   <NA>  <NA>    <NA>
res.liaP[res.liaP$pval.adj < 0.05,"Feature"]
## character(0)
## None here, but you can see that a few phyla are close to sig at 0.06 

res.ds2P <- DA.ds2(TxO_P, predictor = "Type")
## converting counts to integer mode
## using pre-existing size factors
## estimating dispersions
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates
## fitting model and testing
res.ds2P
##    Feature    baseMean log2FoldChange     lfcSE       stat       pval
## 1  ASV1122   0.2162640     -1.5094068 3.1010080 -0.4867472 0.62643752
## 2  ASV1133   2.1332349      3.9165449 1.5677152  2.4982503 0.01248080
## 3  ASV1427   0.1896535      1.2721482 3.1114549  0.4088596 0.68264270
## 4  ASV1814   0.1296656      0.9280411 3.1165397  0.2977793 0.76587160
## 5  ASV1828   0.2162640     -1.5094068 3.1010080 -0.4867472 0.62643752
## 6     ASV2 404.0850186     -1.6166406 0.8160714 -1.9810037 0.04759086
## 7    ASV24  84.6812366      0.2937638 1.0777373  0.2725746 0.78518027
## 8   ASV256  10.0769723      2.1914054 1.6407099  1.3356447 0.18166543
## 9   ASV332   9.7430269     -0.6174584 0.9759300 -0.6326871 0.52693796
## 10  ASV538   0.5203201     -2.5748290 2.6990589 -0.9539729 0.34009735
## 11    ASV6 256.4355836      0.2158250 0.5952578  0.3625741 0.71692307
## 12  ASV806   2.5089056      2.1984062 1.4710593  1.4944376 0.13506129
## 13    ASV9 266.7259972      1.4063539 0.7236906  1.9433082 0.05197893
##             ordering  pval.adj                     Method  Kingdom
## 1  CloacalSwab>Fecal 0.7851803 DESeq2 man. geoMeans (ds2) Bacteria
## 2  Fecal>CloacalSwab 0.1622505 DESeq2 man. geoMeans (ds2) Bacteria
## 3  Fecal>CloacalSwab 0.7851803 DESeq2 man. geoMeans (ds2) Bacteria
## 4  Fecal>CloacalSwab 0.7851803 DESeq2 man. geoMeans (ds2) Bacteria
## 5  CloacalSwab>Fecal 0.7851803 DESeq2 man. geoMeans (ds2) Bacteria
## 6  CloacalSwab>Fecal 0.2252420 DESeq2 man. geoMeans (ds2) Bacteria
## 7  Fecal>CloacalSwab 0.7851803 DESeq2 man. geoMeans (ds2) Bacteria
## 8  Fecal>CloacalSwab 0.4723301 DESeq2 man. geoMeans (ds2) Bacteria
## 9  CloacalSwab>Fecal 0.7851803 DESeq2 man. geoMeans (ds2) Bacteria
## 10 CloacalSwab>Fecal 0.7368776 DESeq2 man. geoMeans (ds2) Bacteria
## 11 Fecal>CloacalSwab 0.7851803 DESeq2 man. geoMeans (ds2) Bacteria
## 12 Fecal>CloacalSwab 0.4389492 DESeq2 man. geoMeans (ds2) Bacteria
## 13 Fecal>CloacalSwab 0.2252420 DESeq2 man. geoMeans (ds2) Bacteria
##                       Phylum Class Order Family Genus Species
## 1               Fusobacteria  <NA>  <NA>   <NA>  <NA>    <NA>
## 2              Acidobacteria  <NA>  <NA>   <NA>  <NA>    <NA>
## 3                Nitrospirae  <NA>  <NA>   <NA>  <NA>    <NA>
## 4             Planctomycetes  <NA>  <NA>   <NA>  <NA>    <NA>
## 5           Gemmatimonadetes  <NA>  <NA>   <NA>  <NA>    <NA>
## 6             Proteobacteria  <NA>  <NA>   <NA>  <NA>    <NA>
## 7  Cyanobacteria/Chloroplast  <NA>  <NA>   <NA>  <NA>    <NA>
## 8                Chloroflexi  <NA>  <NA>   <NA>  <NA>    <NA>
## 9              Bacteroidetes  <NA>  <NA>   <NA>  <NA>    <NA>
## 10       Deinococcus-Thermus  <NA>  <NA>   <NA>  <NA>    <NA>
## 11            Actinobacteria  <NA>  <NA>   <NA>  <NA>    <NA>
## 12           Verrucomicrobia  <NA>  <NA>   <NA>  <NA>    <NA>
## 13                Firmicutes  <NA>  <NA>   <NA>  <NA>    <NA>
res.ds2P[res.ds2P$pval.adj < 0.05,"Feature"]
## character(0)
## Can look at plot again. Surprisingly Proteobacteria nor Bacteroidetes come back as signifant (or near sig) in either of the tests even though they look quite different here. May reflect low sample size...
ggplot(data=Tx_phylum, aes(x=Sample, y=Abundance, fill=Phylum)) +geom_bar(aes(), stat="identity", position="stack")  + 
  ylab("Relative abundance (% of sequences)") +theme_classic() + theme_bw()  +
  theme_classic()+ labs(x = "")+ theme(text = element_text(size = 18)) + scale_fill_manual(values=cbPalette,name="Phylum") + theme(axis.text.x = element_text(angle = 50, vjust = 0.5))

Indicator Species analysis

########       Indicator Species Analysis       ##########
## Run this on the same dataset did for DA testing
## Looking for taxa that distinguish groups. In differential abundance testing above the bacterial taxa may be present in both groups, but the abundance is difference. In the ISA below we are looking for taxa that are generally in one group and not the other. 

TxODA
## phyloseq-class experiment-level object
## otu_table()   OTU Table:         [ 133 taxa and 12 samples ]
## sample_data() Sample Data:       [ 12 samples by 21 sample variables ]
## tax_table()   Taxonomy Table:    [ 133 taxa by 7 taxonomic ranks ]
## 133 taxa found in at least 3 samples

dfTxO_R <- as(sample_data(TxODA), "data.frame")

otu_R <- as.data.frame(t(as(otu_table(TxODA), "matrix")))

### On presence/absence data instead

otu_pa = as.data.frame(ifelse(otu_R>0,1,0))

library(indicspecies)
## 
## Attaching package: 'indicspecies'
## The following object is masked from 'package:Biostrings':
## 
##     coverage
## The following object is masked from 'package:IRanges':
## 
##     coverage
set.seed(714)

## Think about max.order depending on the number of groups you have
indval_pa = multipatt(otu_pa, dfTxO_R$Type, max.order =2, control = how(nperm=999))

summary(indval_pa, indvalcomp = T)
## 
##  Multilevel pattern analysis
##  ---------------------------
## 
##  Association function: IndVal.g
##  Significance level (alpha): 0.05
## 
##  Total number of species: 133
##  Selected number of species: 10 
##  Number of species associated to 1 group: 10 
## 
##  List of species associated to each combination: 
## 
##  Group CloacalSwab  #sps.  3 
##            A      B  stat p.value    
## ASV20 1.0000 1.0000 1.000   0.001 ***
## ASV6  0.8571 1.0000 0.926   0.011 *  
## ASV62 1.0000 0.8333 0.913   0.013 *  
## 
##  Group Fecal  #sps.  7 
##             A      B  stat p.value    
## ASV114 1.0000 1.0000 1.000   0.001 ***
## ASV193 1.0000 1.0000 1.000   0.001 ***
## ASV301 1.0000 1.0000 1.000   0.001 ***
## ASV302 1.0000 1.0000 1.000   0.001 ***
## ASV103 0.8571 1.0000 0.926   0.016 *  
## ASV65  1.0000 0.8333 0.913   0.015 *  
## ASV451 1.0000 0.8333 0.913   0.011 *  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## BUT you need to correct for multiple comparisons
indval_pa$sign
##         s.CloacalSwab s.Fecal index      stat p.value
## ASV6                1       0     1 0.9258201   0.011
## ASV8                1       0     1 0.8164966   0.054
## ASV10               1       0     1 0.7071068   0.171
## ASV11               1       0     1 0.7715167   0.250
## ASV12               1       0     1 0.8164966   0.054
## ASV15               1       1     3 0.6454972      NA
## ASV20               1       0     1 1.0000000   0.001
## ASV22               1       1     3 0.8164966      NA
## ASV26               1       0     1 0.7302967   0.240
## ASV28               1       0     1 0.7071068   0.187
## ASV29               1       1     3 0.5000000      NA
## ASV30               1       1     3 0.8660254      NA
## ASV31               1       0     1 0.7302967   0.232
## ASV34               1       0     1 0.7071068   0.187
## ASV38               1       0     1 0.7071068   0.171
## ASV40               1       0     1 0.8164966   0.058
## ASV43               1       1     3 0.7637626      NA
## ASV44               1       1     3 0.7071068      NA
## ASV47               1       1     3 0.7071068      NA
## ASV53               1       0     1 0.7071068   0.187
## ASV54               0       1     2 0.6123724   0.559
## ASV61               1       1     3 0.5773503      NA
## ASV62               1       0     1 0.9128709   0.013
## ASV65               0       1     2 0.9128709   0.015
## ASV68               1       1     3 0.8164966      NA
## ASV69               1       1     3 0.8164966      NA
## ASV70               1       0     1 0.7302967   0.255
## ASV72               1       1     3 0.7071068      NA
## ASV74               1       1     3 0.5773503      NA
## ASV76               1       0     1 0.8164966   0.064
## ASV81               0       1     2 0.6123724   0.551
## ASV87               1       1     3 0.5773503      NA
## ASV90               1       1     3 0.5000000      NA
## ASV91               0       1     2 0.6123724   0.552
## ASV97               0       1     2 0.6123724   0.552
## ASV100              1       1     3 0.6454972      NA
## ASV103              0       1     2 0.9258201   0.016
## ASV105              0       1     2 0.7715167   0.234
## ASV107              1       0     1 0.8164966   0.054
## ASV114              0       1     2 1.0000000   0.001
## ASV121              1       1     3 0.6454972      NA
## ASV123              1       1     3 0.5000000      NA
## ASV124              1       1     3 0.5000000      NA
## ASV132              1       1     3 0.5000000      NA
## ASV133              1       1     3 0.5000000      NA
## ASV135              1       1     3 0.5773503      NA
## ASV137              1       1     3 0.6454972      NA
## ASV151              1       1     3 0.7071068      NA
## ASV158              1       1     3 0.5773503      NA
## ASV159              1       1     3 0.7071068      NA
## ASV167              1       1     3 0.6454972      NA
## ASV170              1       1     3 0.6454972      NA
## ASV174              1       0     1 0.8333333   0.081
## ASV178              0       1     2 0.6123724   0.542
## ASV183              1       1     3 0.6454972      NA
## ASV190              1       0     1 0.7071068   0.171
## ASV192              0       1     2 0.8333333   0.073
## ASV193              0       1     2 1.0000000   0.001
## ASV194              1       1     3 0.5000000      NA
## ASV196              1       1     3 0.5000000      NA
## ASV199              0       1     2 0.7715167   0.219
## ASV201              1       1     3 0.5000000      NA
## ASV203              1       1     3 0.5000000      NA
## ASV209              0       1     2 0.6123724   0.522
## ASV210              0       1     2 0.6123724   0.529
## ASV215              0       1     2 0.7302967   0.213
## ASV219              0       1     2 0.6123724   0.534
## ASV223              0       1     2 0.8333333   0.075
## ASV232              1       1     3 0.5000000      NA
## ASV238              1       1     3 0.5000000      NA
## ASV241              1       0     1 0.6123724   0.550
## ASV242              1       1     3 0.5000000      NA
## ASV245              0       1     2 0.6123724   0.559
## ASV248              0       1     2 0.7071068   0.182
## ASV250              0       1     2 0.6123724   0.542
## ASV253              0       1     2 0.7302967   0.244
## ASV256              1       1     3 0.5000000      NA
## ASV260              0       1     2 0.7071068   0.182
## ASV264              1       1     3 0.5000000      NA
## ASV267              0       1     2 0.7071068   0.199
## ASV268              0       1     2 0.6123724   0.552
## ASV278              0       1     2 0.7071068   0.182
## ASV281              0       1     2 0.8164966   0.059
## ASV301              0       1     2 1.0000000   0.001
## ASV302              0       1     2 1.0000000   0.001
## ASV303              1       1     3 0.6454972      NA
## ASV309              0       1     2 0.8164966   0.057
## ASV319              0       1     2 0.7302967   0.242
## ASV326              1       1     3 0.5000000      NA
## ASV331              0       1     2 0.6123724   0.549
## ASV332              1       1     3 0.5000000      NA
## ASV340              1       1     3 0.5000000      NA
## ASV343              1       0     1 0.6123724   0.555
## ASV349              0       1     2 0.7071068   0.190
## ASV361              1       0     1 0.6123724   0.531
## ASV375              0       1     2 0.8164966   0.057
## ASV376              1       1     3 0.5000000      NA
## ASV381              1       1     3 0.5000000      NA
## ASV403              0       1     2 0.8164966   0.057
## ASV408              0       1     2 0.6123724   0.549
## ASV451              0       1     2 0.9128709   0.011
## ASV472              0       1     2 0.7071068   0.199
## ASV480              1       1     3 0.5000000      NA
## ASV482              0       1     2 0.8164966   0.057
## ASV483              1       1     3 0.5000000      NA
## ASV489              0       1     2 0.7071068   0.192
## ASV562              0       1     2 0.7071068   0.192
## ASV570              1       1     3 0.5000000      NA
## ASV591              0       1     2 0.8164966   0.056
## ASV665              1       0     1 0.7071068   0.187
## ASV672              0       1     2 0.7071068   0.182
## ASV728              0       1     2 0.8164966   0.064
## ASV759              1       1     3 0.5000000      NA
## ASV762              1       1     3 0.5000000      NA
## ASV784              0       1     2 0.7071068   0.182
## ASV806              0       1     2 0.7071068   0.172
## ASV808              0       1     2 0.7071068   0.175
## ASV819              0       1     2 0.7071068   0.198
## ASV832              0       1     2 0.8164966   0.057
## ASV835              1       1     3 0.5000000      NA
## ASV850              0       1     2 0.7071068   0.172
## ASV851              1       1     3 0.5000000      NA
## ASV884              0       1     2 0.7071068   0.192
## ASV925              1       1     3 0.5000000      NA
## ASV959              0       1     2 0.8164966   0.057
## ASV1107             0       1     2 0.8164966   0.065
## ASV1133             1       1     3 0.5000000      NA
## ASV1155             0       1     2 0.7071068   0.184
## ASV1156             1       1     3 0.5000000      NA
## ASV1180             0       1     2 0.7071068   0.163
## ASV1231             0       1     2 0.7071068   0.193
## ASV1470             1       1     3 0.5000000      NA
## Others              1       1     3 1.0000000      NA
##A -->
# this is the species that only occur in one group, but may not occur in all the replicates

# Faithful to group analysis (B)
# this is the species that occur only in that group and in all replicates
##basically A and B have to both be above 0.7

p_2 <- indval_pa$sign$p.value
## taking p values from that and making it a vector of just p values
p_adj_2 <- round(p.adjust(p_2, "fdr"),3)
## adjusting p values to do multiple comparisons,fdr --> false discovery rate
cbind(p_adj_2,rownames(indval_pa$sign))
##        p_adj_2          
##   [1,] "0.123" "ASV6"   
##   [2,] "0.203" "ASV8"   
##   [3,] "0.293" "ASV10"  
##   [4,] "0.32"  "ASV11"  
##   [5,] "0.203" "ASV12"  
##   [6,] NA      "ASV15"  
##   [7,] "0.016" "ASV20"  
##   [8,] NA      "ASV22"  
##   [9,] "0.317" "ASV26"  
##  [10,] "0.293" "ASV28"  
##  [11,] NA      "ASV29"  
##  [12,] NA      "ASV30"  
##  [13,] "0.317" "ASV31"  
##  [14,] "0.293" "ASV34"  
##  [15,] "0.293" "ASV38"  
##  [16,] "0.203" "ASV40"  
##  [17,] NA      "ASV43"  
##  [18,] NA      "ASV44"  
##  [19,] NA      "ASV47"  
##  [20,] "0.293" "ASV53"  
##  [21,] "0.559" "ASV54"  
##  [22,] NA      "ASV61"  
##  [23,] "0.125" "ASV62"  
##  [24,] "0.125" "ASV65"  
##  [25,] NA      "ASV68"  
##  [26,] NA      "ASV69"  
##  [27,] "0.321" "ASV70"  
##  [28,] NA      "ASV72"  
##  [29,] NA      "ASV74"  
##  [30,] "0.203" "ASV76"  
##  [31,] "0.559" "ASV81"  
##  [32,] NA      "ASV87"  
##  [33,] NA      "ASV90"  
##  [34,] "0.559" "ASV91"  
##  [35,] "0.559" "ASV97"  
##  [36,] NA      "ASV100" 
##  [37,] "0.125" "ASV103" 
##  [38,] "0.317" "ASV105" 
##  [39,] "0.203" "ASV107" 
##  [40,] "0.016" "ASV114" 
##  [41,] NA      "ASV121" 
##  [42,] NA      "ASV123" 
##  [43,] NA      "ASV124" 
##  [44,] NA      "ASV132" 
##  [45,] NA      "ASV133" 
##  [46,] NA      "ASV135" 
##  [47,] NA      "ASV137" 
##  [48,] NA      "ASV151" 
##  [49,] NA      "ASV158" 
##  [50,] NA      "ASV159" 
##  [51,] NA      "ASV167" 
##  [52,] NA      "ASV170" 
##  [53,] "0.226" "ASV174" 
##  [54,] "0.559" "ASV178" 
##  [55,] NA      "ASV183" 
##  [56,] "0.293" "ASV190" 
##  [57,] "0.217" "ASV192" 
##  [58,] "0.016" "ASV193" 
##  [59,] NA      "ASV194" 
##  [60,] NA      "ASV196" 
##  [61,] "0.311" "ASV199" 
##  [62,] NA      "ASV201" 
##  [63,] NA      "ASV203" 
##  [64,] "0.559" "ASV209" 
##  [65,] "0.559" "ASV210" 
##  [66,] "0.308" "ASV215" 
##  [67,] "0.559" "ASV219" 
##  [68,] "0.217" "ASV223" 
##  [69,] NA      "ASV232" 
##  [70,] NA      "ASV238" 
##  [71,] "0.559" "ASV241" 
##  [72,] NA      "ASV242" 
##  [73,] "0.559" "ASV245" 
##  [74,] "0.293" "ASV248" 
##  [75,] "0.559" "ASV250" 
##  [76,] "0.317" "ASV253" 
##  [77,] NA      "ASV256" 
##  [78,] "0.293" "ASV260" 
##  [79,] NA      "ASV264" 
##  [80,] "0.293" "ASV267" 
##  [81,] "0.559" "ASV268" 
##  [82,] "0.293" "ASV278" 
##  [83,] "0.203" "ASV281" 
##  [84,] "0.016" "ASV301" 
##  [85,] "0.016" "ASV302" 
##  [86,] NA      "ASV303" 
##  [87,] "0.203" "ASV309" 
##  [88,] "0.317" "ASV319" 
##  [89,] NA      "ASV326" 
##  [90,] "0.559" "ASV331" 
##  [91,] NA      "ASV332" 
##  [92,] NA      "ASV340" 
##  [93,] "0.559" "ASV343" 
##  [94,] "0.293" "ASV349" 
##  [95,] "0.559" "ASV361" 
##  [96,] "0.203" "ASV375" 
##  [97,] NA      "ASV376" 
##  [98,] NA      "ASV381" 
##  [99,] "0.203" "ASV403" 
## [100,] "0.559" "ASV408" 
## [101,] "0.123" "ASV451" 
## [102,] "0.293" "ASV472" 
## [103,] NA      "ASV480" 
## [104,] "0.203" "ASV482" 
## [105,] NA      "ASV483" 
## [106,] "0.293" "ASV489" 
## [107,] "0.293" "ASV562" 
## [108,] NA      "ASV570" 
## [109,] "0.203" "ASV591" 
## [110,] "0.293" "ASV665" 
## [111,] "0.293" "ASV672" 
## [112,] "0.203" "ASV728" 
## [113,] NA      "ASV759" 
## [114,] NA      "ASV762" 
## [115,] "0.293" "ASV784" 
## [116,] "0.293" "ASV806" 
## [117,] "0.293" "ASV808" 
## [118,] "0.293" "ASV819" 
## [119,] "0.203" "ASV832" 
## [120,] NA      "ASV835" 
## [121,] "0.293" "ASV850" 
## [122,] NA      "ASV851" 
## [123,] "0.293" "ASV884" 
## [124,] NA      "ASV925" 
## [125,] "0.203" "ASV959" 
## [126,] "0.203" "ASV1107"
## [127,] NA      "ASV1133"
## [128,] "0.293" "ASV1155"
## [129,] NA      "ASV1156"
## [130,] "0.293" "ASV1180"
## [131,] "0.293" "ASV1231"
## [132,] NA      "ASV1470"
## [133,] NA      "Others"
table_ISA <- as.data.frame(cbind(p_adj_2,rownames(indval_pa$sign)))

## going to write this table, because using permutations values can change.

write.csv(table_ISA, "ASVs_from_indicator_species.csv")

#my_sigASVs <- read.csv("ASVs_from_indicator_species.csv", header = T, stringsAsFactors = F)

my_sigASVs <- table_ISA[ which(p_adj_2 < 0.05 ),]

my_sigASVs <- my_sigASVs[,2]

## Five ASVs, now let's make sure they had good indicator values
## ASV20  ASV114 ASV193 ASV301 ASV302

summary(indval_pa, indvalcomp = T)
## 
##  Multilevel pattern analysis
##  ---------------------------
## 
##  Association function: IndVal.g
##  Significance level (alpha): 0.05
## 
##  Total number of species: 133
##  Selected number of species: 10 
##  Number of species associated to 1 group: 10 
## 
##  List of species associated to each combination: 
## 
##  Group CloacalSwab  #sps.  3 
##            A      B  stat p.value    
## ASV20 1.0000 1.0000 1.000   0.001 ***
## ASV6  0.8571 1.0000 0.926   0.011 *  
## ASV62 1.0000 0.8333 0.913   0.013 *  
## 
##  Group Fecal  #sps.  7 
##             A      B  stat p.value    
## ASV114 1.0000 1.0000 1.000   0.001 ***
## ASV193 1.0000 1.0000 1.000   0.001 ***
## ASV301 1.0000 1.0000 1.000   0.001 ***
## ASV302 1.0000 1.0000 1.000   0.001 ***
## ASV103 0.8571 1.0000 0.926   0.016 *  
## ASV65  1.0000 0.8333 0.913   0.015 *  
## ASV451 1.0000 0.8333 0.913   0.011 *  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## All have strong indicator stats value > 0.7

tax_table(TxODA)
## Taxonomy Table:     [133 taxa by 7 taxonomic ranks]:
##         Kingdom    Phylum                      Class                
## ASV6    "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV8    "Bacteria" "Proteobacteria"            "Gammaproteobacteria"
## ASV10   "Bacteria" "Proteobacteria"            "Gammaproteobacteria"
## ASV11   "Bacteria" "Proteobacteria"            "Gammaproteobacteria"
## ASV12   "Bacteria" "Cyanobacteria/Chloroplast" "Chloroplast"        
## ASV15   "Bacteria" "Proteobacteria"            "Gammaproteobacteria"
## ASV20   "Bacteria" "Proteobacteria"            "Gammaproteobacteria"
## ASV22   "Bacteria" "Firmicutes"                "Bacilli"            
## ASV26   "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV28   "Bacteria" "Cyanobacteria/Chloroplast" "Chloroplast"        
## ASV29   "Bacteria" "Firmicutes"                "Bacilli"            
## ASV30   "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV31   "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV34   "Bacteria" "Proteobacteria"            "Gammaproteobacteria"
## ASV38   "Bacteria" "Proteobacteria"            "Gammaproteobacteria"
## ASV40   "Bacteria" "Proteobacteria"            "Gammaproteobacteria"
## ASV43   "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV44   "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV47   "Bacteria" "Proteobacteria"            "Gammaproteobacteria"
## ASV53   "Bacteria" "Proteobacteria"            "Gammaproteobacteria"
## ASV54   "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV61   "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV62   "Bacteria" "Firmicutes"                "Bacilli"            
## ASV65   "Bacteria" "Cyanobacteria/Chloroplast" "Chloroplast"        
## ASV68   "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV69   "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV70   "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV72   "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV74   "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV76   "Bacteria" "Proteobacteria"            "Gammaproteobacteria"
## ASV81   "Bacteria" "Firmicutes"                "Clostridia"         
## ASV87   "Bacteria" "Proteobacteria"            "Gammaproteobacteria"
## ASV90   "Bacteria" "Cyanobacteria/Chloroplast" "Chloroplast"        
## ASV91   "Bacteria" "Firmicutes"                "Erysipelotrichia"   
## ASV97   "Bacteria" "Firmicutes"                "Clostridia"         
## ASV100  "Bacteria" "Proteobacteria"            "Alphaproteobacteria"
## ASV103  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV105  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV107  "Bacteria" "Firmicutes"                "Bacilli"            
## ASV114  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV121  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV123  "Bacteria" "Proteobacteria"            "Gammaproteobacteria"
## ASV124  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV132  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV133  "Bacteria" "Chloroflexi"               "Thermomicrobia"     
## ASV135  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV137  "Bacteria" "Firmicutes"                "Erysipelotrichia"   
## ASV151  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV158  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV159  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV167  "Bacteria" "Firmicutes"                "Bacilli"            
## ASV170  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV174  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV178  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV183  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV190  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV192  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV193  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV194  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV196  "Bacteria" "Firmicutes"                "Erysipelotrichia"   
## ASV199  "Bacteria" "Proteobacteria"            "Alphaproteobacteria"
## ASV201  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV203  "Bacteria" "Firmicutes"                "Clostridia"         
## ASV209  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV210  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV215  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV219  "Bacteria" "Proteobacteria"            "Alphaproteobacteria"
## ASV223  "Bacteria" "Proteobacteria"            "Alphaproteobacteria"
## ASV232  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV238  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV241  "Bacteria" "Proteobacteria"            "Alphaproteobacteria"
## ASV242  "Bacteria" "Proteobacteria"            "Gammaproteobacteria"
## ASV245  "Bacteria" "Firmicutes"                "Clostridia"         
## ASV248  "Bacteria" "Firmicutes"                "Clostridia"         
## ASV250  "Bacteria" "Firmicutes"                "Clostridia"         
## ASV253  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV256  "Bacteria" "Chloroflexi"               "Thermomicrobia"     
## ASV260  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV264  "Bacteria" "Firmicutes"                "Clostridia"         
## ASV267  "Bacteria" "Firmicutes"                "Clostridia"         
## ASV268  "Bacteria" "Firmicutes"                "Clostridia"         
## ASV278  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV281  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV301  "Bacteria" "Proteobacteria"            "Alphaproteobacteria"
## ASV302  "Bacteria" "Proteobacteria"            "Alphaproteobacteria"
## ASV303  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV309  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV319  "Bacteria" "Proteobacteria"            "Alphaproteobacteria"
## ASV326  "Bacteria" "Firmicutes"                "Erysipelotrichia"   
## ASV331  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV332  "Bacteria" "Bacteroidetes"             "Bacteroidia"        
## ASV340  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV343  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV349  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV361  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV375  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV376  "Bacteria" "Proteobacteria"            "Betaproteobacteria" 
## ASV381  "Bacteria" "Firmicutes"                "Clostridia"         
## ASV403  "Bacteria" "Proteobacteria"            "Alphaproteobacteria"
## ASV408  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV451  "Bacteria" "Proteobacteria"            "Alphaproteobacteria"
## ASV472  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV480  "Bacteria" "Firmicutes"                "Clostridia"         
## ASV482  "Bacteria" "Proteobacteria"            "Alphaproteobacteria"
## ASV483  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV489  "Bacteria" "Proteobacteria"            "Alphaproteobacteria"
## ASV562  "Bacteria" "Proteobacteria"            "Alphaproteobacteria"
## ASV570  "Bacteria" "Proteobacteria"            "Alphaproteobacteria"
## ASV591  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV665  "Bacteria" "Proteobacteria"            "Alphaproteobacteria"
## ASV672  "Bacteria" "Chloroflexi"               NA                   
## ASV728  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV759  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV762  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV784  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV806  "Bacteria" "Verrucomicrobia"           "Spartobacteria"     
## ASV808  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV819  "Bacteria" "Bacteroidetes"             "Bacteroidia"        
## ASV832  "Bacteria" "Proteobacteria"            "Alphaproteobacteria"
## ASV835  "Bacteria" "Verrucomicrobia"           "Spartobacteria"     
## ASV850  "Bacteria" "Proteobacteria"            "Alphaproteobacteria"
## ASV851  "Bacteria" "Proteobacteria"            "Alphaproteobacteria"
## ASV884  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV925  "Bacteria" "Firmicutes"                "Clostridia"         
## ASV959  "Bacteria" "Proteobacteria"            "Alphaproteobacteria"
## ASV1107 "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV1133 "Bacteria" "Acidobacteria"             "Acidobacteria_Gp16" 
## ASV1155 "Bacteria" "Proteobacteria"            "Alphaproteobacteria"
## ASV1156 "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV1180 "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV1231 "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV1470 "Bacteria" "Chloroflexi"               "Chloroflexia"       
## Others  NA         NA                          NA                   
##         Order                                Family                
## ASV6    "Actinomycetales"                    "Sanguibacteraceae"   
## ASV8    "Pseudomonadales"                    "Pseudomonadaceae"    
## ASV10   "Oceanospirillales"                  "Halomonadaceae"      
## ASV11   "Enterobacteriales"                  "Enterobacteriaceae"  
## ASV12   "Chloroplast"                        "Streptophyta"        
## ASV15   "Enterobacteriales"                  "Enterobacteriaceae"  
## ASV20   "Pseudomonadales"                    "Pseudomonadaceae"    
## ASV22   "Lactobacillales"                    "Enterococcaceae"     
## ASV26   "Actinomycetales"                    "Pseudonocardiaceae"  
## ASV28   "Chloroplast"                        "Streptophyta"        
## ASV29   "Lactobacillales"                    "Carnobacteriaceae"   
## ASV30   "Solirubrobacterales"                "Patulibacteraceae"   
## ASV31   "Actinomycetales"                    "Propionibacteriaceae"
## ASV34   "Pseudomonadales"                    "Pseudomonadaceae"    
## ASV38   "Pseudomonadales"                    "Pseudomonadaceae"    
## ASV40   "Pseudomonadales"                    "Moraxellaceae"       
## ASV43   "Actinomycetales"                    "Pseudonocardiaceae"  
## ASV44   "Actinomycetales"                    "Microbacteriaceae"   
## ASV47   "Enterobacteriales"                  "Enterobacteriaceae"  
## ASV53   "Pseudomonadales"                    "Moraxellaceae"       
## ASV54   "Coriobacteriales"                   "Coriobacteriaceae"   
## ASV61   "Actinomycetales"                    NA                    
## ASV62   "Bacillales"                         "Staphylococcaceae"   
## ASV65   "Chloroplast"                        "Chlorophyta"         
## ASV68   "Actinomycetales"                    "Mycobacteriaceae"    
## ASV69   "Actinomycetales"                    "Nocardiaceae"        
## ASV70   "Actinomycetales"                    "Pseudonocardiaceae"  
## ASV72   "Actinomycetales"                    "Pseudonocardiaceae"  
## ASV74   "Actinomycetales"                    "Propionibacteriaceae"
## ASV76   "Pseudomonadales"                    "Pseudomonadaceae"    
## ASV81   "Clostridiales"                      "Ruminococcaceae"     
## ASV87   "Enterobacteriales"                  "Enterobacteriaceae"  
## ASV90   "Chloroplast"                        "Streptophyta"        
## ASV91   "Erysipelotrichales"                 "Erysipelotrichaceae" 
## ASV97   "Clostridiales"                      "Lachnospiraceae"     
## ASV100  "Rhizobiales"                        "Methylobacteriaceae" 
## ASV103  "Solirubrobacterales"                "Solirubrobacteraceae"
## ASV105  "Actinomycetales"                    "Pseudonocardiaceae"  
## ASV107  "Lactobacillales"                    "Carnobacteriaceae"   
## ASV114  "Solirubrobacterales"                "Solirubrobacteraceae"
## ASV121  "Actinomycetales"                    "Microbacteriaceae"   
## ASV123  "Enterobacteriales"                  "Enterobacteriaceae"  
## ASV124  "Actinomycetales"                    "Mycobacteriaceae"    
## ASV132  "Actinomycetales"                    "Microbacteriaceae"   
## ASV133  "Sphaerobacterales"                  "Sphaerobacteraceae"  
## ASV135  "Solirubrobacterales"                "Solirubrobacteraceae"
## ASV137  "Erysipelotrichales"                 "Erysipelotrichaceae" 
## ASV151  "Actinomycetales"                    "Mycobacteriaceae"    
## ASV158  "Actinomycetales"                    "Nocardioidaceae"     
## ASV159  "Actinomycetales"                    "Microbacteriaceae"   
## ASV167  "Bacillales"                         "Bacillaceae_1"       
## ASV170  "Actinomycetales"                    "Microbacteriaceae"   
## ASV174  "Actinomycetales"                    "Microbacteriaceae"   
## ASV178  "Actinomycetales"                    "Intrasporangiaceae"  
## ASV183  "Actinomycetales"                    "Nocardioidaceae"     
## ASV190  "Actinomycetales"                    "Microbacteriaceae"   
## ASV192  "Rubrobacterales"                    "Rubrobacteraceae"    
## ASV193  "Rubrobacterales"                    "Rubrobacteraceae"    
## ASV194  "Actinomycetales"                    "Mycobacteriaceae"    
## ASV196  "Erysipelotrichales"                 "Erysipelotrichaceae" 
## ASV199  "Rhizobiales"                        "Methylobacteriaceae" 
## ASV201  "Actinomycetales"                    "Nocardioidaceae"     
## ASV203  "Clostridiales"                      "Lachnospiraceae"     
## ASV209  "Actinomycetales"                    "Nocardioidaceae"     
## ASV210  "Solirubrobacterales"                "Solirubrobacteraceae"
## ASV215  "Actinomycetales"                    "Propionibacteriaceae"
## ASV219  "Rhizobiales"                        "Methylobacteriaceae" 
## ASV223  "Rhizobiales"                        "Bradyrhizobiaceae"   
## ASV232  "Actinomycetales"                    "Nocardioidaceae"     
## ASV238  "Actinomycetales"                    "Nocardioidaceae"     
## ASV241  "Rhizobiales"                        "Methylobacteriaceae" 
## ASV242  "Enterobacteriales"                  "Enterobacteriaceae"  
## ASV245  "Clostridiales"                      "Ruminococcaceae"     
## ASV248  "Clostridiales"                      "Eubacteriaceae"      
## ASV250  "Clostridiales"                      "Lachnospiraceae"     
## ASV253  "Gaiellales"                         "Gaiellaceae"         
## ASV256  "Sphaerobacterales"                  "Sphaerobacteraceae"  
## ASV260  "Actinomycetales"                    "Pseudonocardiaceae"  
## ASV264  "Clostridiales"                      "Ruminococcaceae"     
## ASV267  "Clostridiales"                      "Lachnospiraceae"     
## ASV268  "Clostridiales"                      "Lachnospiraceae"     
## ASV278  "Actinomycetales"                    "Propionibacteriaceae"
## ASV281  "Actinomycetales"                    NA                    
## ASV301  "Alphaproteobacteria_incertae_sedis" "Geminicoccus"        
## ASV302  "Rhizobiales"                        "Rhodobiaceae"        
## ASV303  "Actinomycetales"                    "Streptomycetaceae"   
## ASV309  NA                                   NA                    
## ASV319  "Rhizobiales"                        "Methylobacteriaceae" 
## ASV326  "Erysipelotrichales"                 "Erysipelotrichaceae" 
## ASV331  "Solirubrobacterales"                NA                    
## ASV332  "Bacteroidales"                      "Bacteroidaceae"      
## ASV340  "Actinomycetales"                    "Pseudonocardiaceae"  
## ASV343  "Actinomycetales"                    "Mycobacteriaceae"    
## ASV349  "Actinomycetales"                    "Cellulomonadaceae"   
## ASV361  "Actinomycetales"                    "Pseudonocardiaceae"  
## ASV375  "Solirubrobacterales"                "Conexibacteraceae"   
## ASV376  "Burkholderiales"                    "Alcaligenaceae"      
## ASV381  "Clostridiales"                      "Ruminococcaceae"     
## ASV403  "Rhizobiales"                        "Methylobacteriaceae" 
## ASV408  "Actinomycetales"                    NA                    
## ASV451  "Rhizobiales"                        "Methylobacteriaceae" 
## ASV472  "Actinomycetales"                    "Kineosporiaceae"     
## ASV480  "Clostridiales"                      "Ruminococcaceae"     
## ASV482  "Alphaproteobacteria_incertae_sedis" "Geminicoccus"        
## ASV483  "Actinomycetales"                    "Micrococcaceae"      
## ASV489  "Rhodospirillales"                   "Reyranella"          
## ASV562  "Rhizobiales"                        "Hyphomicrobiaceae"   
## ASV570  "Rhizobiales"                        "Methylobacteriaceae" 
## ASV591  "Solirubrobacterales"                "Solirubrobacteraceae"
## ASV665  "Sphingomonadales"                   "Sphingomonadaceae"   
## ASV672  NA                                   NA                    
## ASV728  "Acidimicrobiales"                   "Acidimicrobiaceae"   
## ASV759  "Actinomycetales"                    "Propionibacteriaceae"
## ASV762  "Acidimicrobiales"                   "Acidimicrobiaceae"   
## ASV784  "Actinomycetales"                    "Intrasporangiaceae"  
## ASV806  "Terrimicrobium"                     NA                    
## ASV808  "Gaiellales"                         "Gaiellaceae"         
## ASV819  "Bacteroidales"                      "Bacteroidaceae"      
## ASV832  "Alphaproteobacteria_incertae_sedis" "Geminicoccus"        
## ASV835  "Terrimicrobium"                     NA                    
## ASV850  "Rhizobiales"                        "Hyphomicrobiaceae"   
## ASV851  "Alphaproteobacteria_incertae_sedis" "Geminicoccus"        
## ASV884  "Solirubrobacterales"                NA                    
## ASV925  "Clostridiales"                      "Lachnospiraceae"     
## ASV959  "Alphaproteobacteria_incertae_sedis" "Geminicoccus"        
## ASV1107 "Solirubrobacterales"                NA                    
## ASV1133 "Gp16"                               NA                    
## ASV1155 "Rhizobiales"                        "Xanthobacteraceae"   
## ASV1156 "Solirubrobacterales"                "Solirubrobacteraceae"
## ASV1180 "Actinomycetales"                    "Nocardioidaceae"     
## ASV1231 "Rubrobacterales"                    "Rubrobacteraceae"    
## ASV1470 "Kallotenuales"                      "Kallotenuaceae"      
## Others  NA                                   NA                    
##         Genus               Species         
## ASV6    "Sanguibacter"      NA              
## ASV8    "Pseudomonas"       NA              
## ASV10   "Salinicola"        "socius"        
## ASV11   "Buttiauxella"      NA              
## ASV12   NA                  NA              
## ASV15   "Enterobacter"      NA              
## ASV20   "Pseudomonas"       NA              
## ASV22   "Enterococcus"      NA              
## ASV26   "Actinomycetospora" NA              
## ASV28   NA                  NA              
## ASV29   "Catellicoccus"     NA              
## ASV30   "Patulibacter"      "minatonensis"  
## ASV31   "Friedmanniella"    NA              
## ASV34   "Pseudomonas"       NA              
## ASV38   "Pseudomonas"       NA              
## ASV40   "Acinetobacter"     NA              
## ASV43   "Pseudonocardia"    "endophytica"   
## ASV44   "Microbacterium"    NA              
## ASV47   "Pantoea"           NA              
## ASV53   "Acinetobacter"     NA              
## ASV54   "Denitrobacterium"  NA              
## ASV61   NA                  NA              
## ASV62   "Staphylococcus"    NA              
## ASV65   NA                  NA              
## ASV68   "Mycobacterium"     NA              
## ASV69   "Rhodococcus"       NA              
## ASV70   "Actinomycetospora" "chiangmaiensis"
## ASV72   "Actinomycetospora" NA              
## ASV74   NA                  NA              
## ASV76   "Pseudomonas"       NA              
## ASV81   "Intestinimonas"    NA              
## ASV87   "Pantoea"           NA              
## ASV90   NA                  NA              
## ASV91   "Clostridium_XVIII" NA              
## ASV97   NA                  NA              
## ASV100  "Methylobacterium"  NA              
## ASV103  "Solirubrobacter"   NA              
## ASV105  "Actinomycetospora" NA              
## ASV107  "Carnobacterium"    NA              
## ASV114  "Solirubrobacter"   NA              
## ASV121  "Agrococcus"        NA              
## ASV123  NA                  NA              
## ASV124  "Mycobacterium"     NA              
## ASV132  "Curtobacterium"    NA              
## ASV133  NA                  NA              
## ASV135  "Solirubrobacter"   NA              
## ASV137  "Clostridium_XVIII" NA              
## ASV151  "Mycobacterium"     "JC2972"        
## ASV158  "Nocardioides"      NA              
## ASV159  "Microbacterium"    NA              
## ASV167  "Bacillus"          NA              
## ASV170  "Curtobacterium"    NA              
## ASV174  "Microbacterium"    NA              
## ASV178  NA                  NA              
## ASV183  "Nocardioides"      NA              
## ASV190  "Pseudoclavibacter" "helvolus"      
## ASV192  "Rubrobacter"       NA              
## ASV193  "Rubrobacter"       NA              
## ASV194  "Mycobacterium"     NA              
## ASV196  "Clostridium_XVIII" NA              
## ASV199  NA                  NA              
## ASV201  "Nocardioides"      NA              
## ASV203  NA                  NA              
## ASV209  "Nocardioides"      "ginsengagri"   
## ASV210  "Solirubrobacter"   NA              
## ASV215  "Microlunatus"      NA              
## ASV219  NA                  NA              
## ASV223  "Bradyrhizobium"    NA              
## ASV232  "Nocardioides"      NA              
## ASV238  "Nocardioides"      NA              
## ASV241  "Methylobacterium"  NA              
## ASV242  "Pantoea"           NA              
## ASV245  "Intestinimonas"    NA              
## ASV248  "Anaerofustis"      NA              
## ASV250  NA                  NA              
## ASV253  "Gaiella"           NA              
## ASV256  "Sphaerobacter"     NA              
## ASV260  "Pseudonocardia"    NA              
## ASV264  NA                  NA              
## ASV267  "Clostridium_XlVa"  NA              
## ASV268  NA                  NA              
## ASV278  "Microlunatus"      NA              
## ASV281  NA                  NA              
## ASV301  NA                  NA              
## ASV302  NA                  NA              
## ASV303  "Streptomyces"      NA              
## ASV309  NA                  NA              
## ASV319  "Microvirga"        "zambiensis"    
## ASV326  "Clostridium_XVIII" NA              
## ASV331  NA                  NA              
## ASV332  "Bacteroides"       NA              
## ASV340  "Pseudonocardia"    NA              
## ASV343  "Mycobacterium"     NA              
## ASV349  "Cellulomonas"      NA              
## ASV361  "Pseudonocardia"    NA              
## ASV375  "Conexibacter"      NA              
## ASV376  "Achromobacter"     NA              
## ASV381  "Anaerofilum"       NA              
## ASV403  "Microvirga"        NA              
## ASV408  NA                  NA              
## ASV451  "Microvirga"        NA              
## ASV472  "Pseudokineococcus" NA              
## ASV480  "Clostridium_IV"    NA              
## ASV482  NA                  NA              
## ASV483  "Arthrobacter"      NA              
## ASV489  NA                  NA              
## ASV562  "Rhodoplanes"       NA              
## ASV570  "Microvirga"        "lotononidis"   
## ASV591  "Solirubrobacter"   NA              
## ASV665  "Sphingopyxis"      NA              
## ASV672  NA                  NA              
## ASV728  "Ilumatobacter"     NA              
## ASV759  "Friedmanniella"    NA              
## ASV762  "Ilumatobacter"     NA              
## ASV784  "Janibacter"        NA              
## ASV806  NA                  NA              
## ASV808  "Gaiella"           NA              
## ASV819  "Bacteroides"       NA              
## ASV832  NA                  NA              
## ASV835  NA                  NA              
## ASV850  "Pedomicrobium"     NA              
## ASV851  NA                  NA              
## ASV884  NA                  NA              
## ASV925  "Clostridium_XlVa"  NA              
## ASV959  NA                  NA              
## ASV1107 NA                  NA              
## ASV1133 NA                  NA              
## ASV1155 NA                  NA              
## ASV1156 "Solirubrobacter"   NA              
## ASV1180 "Nocardioides"      NA              
## ASV1231 "Rubrobacter"       NA              
## ASV1470 "Kallotenue"        NA              
## Others  NA                  NA
## Need an OTU ID in the taxonomy table to match to
tax_table(TxODA) <- cbind(tax_table(TxODA), ASV=taxa_names(TxODA))
head(tax_table(TxODA))
## Taxonomy Table:     [6 taxa by 8 taxonomic ranks]:
##       Kingdom    Phylum                      Class                
## ASV6  "Bacteria" "Actinobacteria"            "Actinobacteria"     
## ASV8  "Bacteria" "Proteobacteria"            "Gammaproteobacteria"
## ASV10 "Bacteria" "Proteobacteria"            "Gammaproteobacteria"
## ASV11 "Bacteria" "Proteobacteria"            "Gammaproteobacteria"
## ASV12 "Bacteria" "Cyanobacteria/Chloroplast" "Chloroplast"        
## ASV15 "Bacteria" "Proteobacteria"            "Gammaproteobacteria"
##       Order               Family               Genus          Species 
## ASV6  "Actinomycetales"   "Sanguibacteraceae"  "Sanguibacter" NA      
## ASV8  "Pseudomonadales"   "Pseudomonadaceae"   "Pseudomonas"  NA      
## ASV10 "Oceanospirillales" "Halomonadaceae"     "Salinicola"   "socius"
## ASV11 "Enterobacteriales" "Enterobacteriaceae" "Buttiauxella" NA      
## ASV12 "Chloroplast"       "Streptophyta"       NA             NA      
## ASV15 "Enterobacteriales" "Enterobacteriaceae" "Enterobacter" NA      
##       ASV    
## ASV6  "ASV6" 
## ASV8  "ASV8" 
## ASV10 "ASV10"
## ASV11 "ASV11"
## ASV12 "ASV12"
## ASV15 "ASV15"
Select_my_sigASVs <-  subset_taxa(TxODA, ASV %in% my_sigASVs)

tax_table(Select_my_sigASVs)
## Taxonomy Table:     [5 taxa by 8 taxonomic ranks]:
##        Kingdom    Phylum           Class                
## ASV20  "Bacteria" "Proteobacteria" "Gammaproteobacteria"
## ASV114 "Bacteria" "Actinobacteria" "Actinobacteria"     
## ASV193 "Bacteria" "Actinobacteria" "Actinobacteria"     
## ASV301 "Bacteria" "Proteobacteria" "Alphaproteobacteria"
## ASV302 "Bacteria" "Proteobacteria" "Alphaproteobacteria"
##        Order                                Family                
## ASV20  "Pseudomonadales"                    "Pseudomonadaceae"    
## ASV114 "Solirubrobacterales"                "Solirubrobacteraceae"
## ASV193 "Rubrobacterales"                    "Rubrobacteraceae"    
## ASV301 "Alphaproteobacteria_incertae_sedis" "Geminicoccus"        
## ASV302 "Rhizobiales"                        "Rhodobiaceae"        
##        Genus             Species ASV     
## ASV20  "Pseudomonas"     NA      "ASV20" 
## ASV114 "Solirubrobacter" NA      "ASV114"
## ASV193 "Rubrobacter"     NA      "ASV193"
## ASV301 NA                NA      "ASV301"
## ASV302 NA                NA      "ASV302"
ASV20 <- subset_taxa(TxODA, ASV == "ASV20")

plot_bar(ASV20, "Type", "Abundance")
## Warning in psmelt(physeq): The sample variables: 
## Species
##  have been renamed to: 
## sample_Species
## to avoid conflicts with taxonomic rank names.

## Looks like found in 6 samples of cloaca (each stack is a sample), and none in fecal

ASV301 <- subset_taxa(TxODA, ASV == "ASV301")
plot_bar(ASV301, "Type", "Abundance")
## Warning in psmelt(physeq): The sample variables: 
## Species
##  have been renamed to: 
## sample_Species
## to avoid conflicts with taxonomic rank names.

## This is the reverse, 6 samples fecal and none in cloacal. Family Geminicoccus is this ASV. 




##### THE END (for now ;)) #######